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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/d0cca96d8591568669d8b395a1da9b7aa5d7c2f4">d0cca96d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-23T21:39:01+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.17</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/0abd8ffdbc18b5f6a8deeb4c73967423667b04fb">0abd8ffd</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-23T21:39:01+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.3.17'
Update to upstream version '1.3.17'
with Debian dir 373d1b637b885f9952fd82cad3569a63d0e25b4b</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/97b5faf0bd92f7f493f9007ec81ec23752e9734e">97b5faf0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-23T21:40:05+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
</li>
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<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
align.c
</a>
</li>
<li class="file-stats">
<a href="#6abbb3f721a6a2755259d4b75d5f59fbc6d160c1">
align.h
</a>
</li>
<li class="file-stats">
<a href="#596ab94993f840fb54df19a92f10da821eccfa7a">
chain.c
</a>
</li>
<li class="file-stats">
<a href="#f966218212bf61b9bacc17a9bc23ef9ad756be7c">
chain.h
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#5bb411548ec4b39482e6de83d3ad98f29b1162b1">
kma.c
</a>
</li>
<li class="file-stats">
<a href="#97e3379ce2e33418ea5b83d3faaf35326b973d41">
nw.c
</a>
</li>
<li class="file-stats">
<a href="#61a960d3b9862f2e47015c82850b2b590c708d06">
nw.h
</a>
</li>
<li class="file-stats">
<a href="#24b1ddd54f1e7a0b2170af91261c0ecfa055c98d">
runinput.c
</a>
</li>
<li class="file-stats">
<a href="#04f591434765972061a4501d514d48d8e013bc2a">
runinput.h
</a>
</li>
<li class="file-stats">
<a href="#47c9f6f4145bb3c988501538a8d789c80635121f">
stdnuc.h
</a>
</li>
<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
<a href="https://salsa.debian.org/med-team/kma/-/compare/3a0c2e0868ae672f84c60fafa3bcea1aa87ca059...97b5faf0bd92f7f493f9007ec81ec23752e9734e#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40"><strong>align.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,180 @@</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdnuc.h"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdstat.h"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">leadTailAlnPtr</span><span class="p">)(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <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;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</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;">leadTailAln</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trailTailAlnPtr</span><span class="p">)(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">AlnScore</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</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;">trailTailAln</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">skipLeadAln</span><span class="p">(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> </span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">AlnScore</span> <span class="n" style="color: #333;">Stat</span><span class="p">;</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* initialize */</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</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="LC40" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</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="LC41" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</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="LC42" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</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="LC43" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</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="LC44" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_e</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Stat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">leadTailAln</span><span class="p">(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</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;">AlnScore</span> <span class="n" style="color: #333;">Stat</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* initialize */</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</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="LC56" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</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="LC57" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</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="LC58" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</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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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</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="LC60" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_e</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_e</span><span class="p">)</span> <span class="p">{</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get boundaries */</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="n" style="color: #333;">t_s</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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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> <span class="n" style="color: #333;">q_s</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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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">t_e</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big leading template gap, cut down</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//t_s = t_e - MIN(bandwidth, (q_e << 1));</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" 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;">t_e</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">q_e</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big leading query gap, cut down</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//q_s = q_e - MIN(bandwidth, (t_e << 1));</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="p">}</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"> </span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* align */</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</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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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">;</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">// || abs(t_e - t_s - q_e - q_s) >= 32) {</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW</span><span class="p">(</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_s</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;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_score</span><span class="p">(</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_s</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;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC83" 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;">Frag_align</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band</span><span class="p">(</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_s</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;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat = NW(tseq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, Frag_align, matrices, t_len);</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band_score</span><span class="p">(</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_s</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;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat = NW_score(tseq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, matrices, t_len);</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim leading gaps */</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">bias</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="LC94" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_s</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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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="p">}</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bias</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="c"> <span class="p">}</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*if(bias) {</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> NWstat.score -= (W1 + (bias - 1) * U);</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="p">}</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"> </span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</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;">Frag_align</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;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="p">}</span> </span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">);</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" 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;">aligned</span><span class="p">)</span> <span class="p">{</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_s</span><span class="p">;</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"> <span class="p">}</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="p">}</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> </span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Stat</span><span class="p">;</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"><span class="p">}</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">skipTrailAln</span><span class="p">(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">AlnScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Stat</span><span class="p">,</span> <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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</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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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> <span class="p">}</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"><span class="p">}</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">trailTailAln</span><span class="p">(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">AlnScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Stat</span><span class="p">,</span> <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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> </span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">;</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">AlnScore</span> <span class="n" style="color: #333;">NWstat</span><span class="p">;</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> </span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get intervals in query and template to align */</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span><span class="p">;</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(((</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big trailing template gap, cut down</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//t_e = t_s + MIN(bandwidth, ((q_len - q_s) << 1));</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">;</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" 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;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big leading query gap, cut down</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//q_e = q_s + MIN(bandwidth, ((t_len - t_s) << 1));</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</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="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> <span class="p">}</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"> </span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* align trailing gap */</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</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="LC155" class="line" lang="c"> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//|| abs(t_e - t_s - q_e - q_s) >= 32) {</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</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="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW</span><span class="p">(</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t_len</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</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="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_score</span><span class="p">(</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t_len</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</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="c"> <span class="p">}</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" 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;">Frag_align</span><span class="p">)</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="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band</span><span class="p">(</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t_len</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat = NW(tseq, qseq, 1 + (t_e == t_len), t_s, t_e, q_s, q_e, Frag_align, matrices, t_len);</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band_score</span><span class="p">(</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t_len</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</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="c"> <span class="p">}</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"> </span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="p">)</span> <span class="p">{</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim trailing gaps */</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t_len</span><span class="p">)</span> <span class="p">{</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</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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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">)</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="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> <span class="p">}</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"> <span class="p">}</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bias</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="c"> </span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">)</span> <span class="p">{</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat.score -= (W1 + (NWstat.len - bias) * U);</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bias</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="c"> <span class="p">}</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="c"> <span class="p">}</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="c"> </span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Stat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</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;">Stat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</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;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="192" 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">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Stat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC200" 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;">Frag_align</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</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="LC202" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">KMA</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_end</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</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">@@ -227,75 +401,10 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"> <span class="p">}</span></span>
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim seeds */</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="c"> <span class="n" style="color: #333;">trimSeeds</span><span class="p">(</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* initialize */</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</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="LC234" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</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="LC235" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</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="LC236" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</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="LC237" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</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="LC238" class="line" lang="c"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</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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<pre style="margin: 0;">-<span id="LC239" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="c"> <span class="n" style="color: #333;">trimSeedsPtr</span><span class="p">(</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* align leading tail */</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get boundaries */</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">t_s</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="LC246" class="line" lang="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="c"> <span class="n" style="color: #333;">q_s</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="LC248" class="line" lang="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">t_e</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big leading template gap, cut down</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//t_s = t_e - MIN(bandwidth, (q_e << 1));</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC252" 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;">t_e</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">q_e</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big leading query gap, cut down</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//q_s = q_e - MIN(bandwidth, (t_e << 1));</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* align */</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</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="LC259" class="line" lang="c"> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">// || abs(t_e - t_s - q_e - q_s) >= 32) {</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_s</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;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_s</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;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat = NW(template_index->seq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, Frag_align, matrices);</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="c"> <span class="p">}</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c"> </span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim leading gaps */</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="c"> <span class="n" style="color: #333;">bias</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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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_s</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="LC270" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*if(bias) {</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> NWstat.score -= (W1 + (bias - 1) * U);</span></span>
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<pre style="margin: 0;">-<span id="LC282" 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="LC283" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</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;">Frag_align</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;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">leadTailAlnPtr</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</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;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">],</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* piece seeds together */</span></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="c"> <span class="n" style="color: #333;">stop</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -357,11 +466,11 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Stat</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">t_l</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</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="LC360" class="line" lang="c"> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">4</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t_l</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="c"> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t_l</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">t_l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">// || abs(t_e - t_s - q_e - q_s) >= 32) {</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">t_len</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">t_len</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat = NW(template_index->seq, qseq, 0, t_s, t_e, q_s, q_e, Frag_align, matrices);</span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="c"> </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">@@ -380,63 +489,7 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* align trailing tail */</span></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get intervals in query and template to align */</span></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="c"> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="c"> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</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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<pre style="margin: 0;">-<span id="LC386" class="line" lang="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(((</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big trailing template gap, cut down</span></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//t_e = t_s + MIN(bandwidth, ((q_len - q_s) << 1));</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">;</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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392
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<td class="new_line diff-line-num old" data-linenumber="492" 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="LC392" 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;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big leading query gap, cut down</span></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//q_e = q_s + MIN(bandwidth, ((t_len - t_s) << 1));</span></span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">;</span></span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="c"> <span class="p">}</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="c"> </span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* align trailing gap */</span></span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</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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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="c"> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//|| abs(t_e - t_s - q_e - q_s) >= 32) {</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t_len</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t_len</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat = NW(template_index->seq, qseq, 1 + (t_e == t_len), t_s, t_e, q_s, q_e, Frag_align, matrices);</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim trailing gaps */</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t_len</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="c"> <span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</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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<pre style="margin: 0;">-<span id="LC410" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat.score -= (W1 + (NWstat.len - bias) * U);</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="c"> </span>
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428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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429
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</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;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</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;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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430
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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432
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="c"> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</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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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="c"> <span class="p">}</span></span>
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439
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="c"> </span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="c"> <span class="n" style="color: #333;">trailTailAlnPtr</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Stat</span><span class="p">,</span> <span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</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;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">],</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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440
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="c"> <span class="n" style="color: #333;">aligned</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;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">]</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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441
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494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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442
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495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</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">@@ -450,7 +503,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</span><span class="p">;</span></span>
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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452
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_l</span><span class="p">,</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">mem_count</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seeds</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">mapQ</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">mapQ</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cPos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">iPos</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="c"> <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;">key</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nuc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="c"> <span class="n" style="color: #333;">AlnScore</span> <span class="n" style="color: #333;">Stat</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="531" style="width: 35px; color: rgba(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">@@ -478,7 +531,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</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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<pre style="margin: 0;"> <span id="LC532" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">key</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;">getKmer</span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="c"> <span class="n" style="color: #333;">getKmer<span class="idiff left">_macro</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">cPos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">iPos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">shifter</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="c"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashMapCCI_get</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">value</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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="629" style="width: 35px; color: rgba(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">@@ -576,6 +629,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq_comp</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;">i</span><span class="p">]</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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<pre style="margin: 0;"> <span id="LC630" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="c"> <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="LC633" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mem_count</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mem_count</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">@@ -593,8 +647,6 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get best seed chain, returns best starting point */</span></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chainSeedsPtr</span><span class="p">(</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mapQ</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if(score < (q_len >> 5)) {</span></span>
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mapQ</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</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="LC652" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -606,48 +658,8 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Stat</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* initialize */</span></span>
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610
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</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="LC611" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</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="LC612" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</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="LC613" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</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="LC614" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</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="LC615" class="line" lang="c"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</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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616
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</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="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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618
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* align leading tail */</span></span>
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620
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</span> <span class="p">{</span></span>
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621
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get boundaries */</span></span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="c"> <span class="n" style="color: #333;">t_s</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="LC623" class="line" lang="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="c"> <span class="n" style="color: #333;">q_s</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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625
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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626
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">t_e</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big leading template gap, cut down</span></span>
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627
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//t_s = t_e - MIN(bandwidth, (q_e << 1));</span></span>
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628
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="c"> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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629
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<pre style="margin: 0;">-<span id="LC629" 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;">t_e</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">q_e</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big leading query gap, cut down</span></span>
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630
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//q_s = q_e - MIN(bandwidth, (t_e << 1));</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="c"> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* align */</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</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="LC636" class="line" lang="c"> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">// || abs(t_e - t_s - q_e - q_s) >= 32) {</span></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_score</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_s</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;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band_score</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_s</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;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat = NW_score(template_index->seq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, matrices, t_len);</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">leadTailAlnPtr</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;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</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;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">],</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* piece seeds together */</span></span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="c"> <span class="n" style="color: #333;">stop</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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<td class="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -703,7 +715,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Stat</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">t_l</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</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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706
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="c"> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">4</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t_l</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="c"> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t_l</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">t_l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_score</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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">@@ -721,35 +733,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* align trailing tail */</span></span>
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get intervals in query and template to align */</span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="c"> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="c"> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</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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<pre style="margin: 0;">-<span id="LC727" class="line" lang="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</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="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="p">((</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big trailing template gap, cut down</span></span>
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730
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//t_e = t_s + MIN(bandwidth, ((q_len - q_s) << 1));</span></span>
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731
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">;</span></span>
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732
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="c"> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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733
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<td class="new_line diff-line-num old" data-linenumber="736" 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="LC733" 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;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="p">((</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// big leading query gap, cut down</span></span>
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734
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//q_e = q_s + MIN(bandwidth, ((t_len - t_s) << 1));</span></span>
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735
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">;</span></span>
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736
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<td class="new_line diff-line-num old" data-linenumber="736" 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="LC736" class="line" lang="c"> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">));</span></span>
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737
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="c"> <span class="p">}</span></span>
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738
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="c"> </span>
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739
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<td class="new_line diff-line-num old" data-linenumber="736" 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="LC739" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* align trailing gap */</span></span>
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740
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</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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<td class="old_line diff-line-num old" data-linenumber="741" 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">
741
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="c"> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bandwidth</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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">band</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//|| abs(t_e - t_s - q_e - q_s) >= 32) {</span></span>
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_score</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t_len</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band_score</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</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;">t_e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t_len</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC752" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="c"> <span class="n" style="color: #333;">trailTailAlnPtr</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Stat</span><span class="p">,</span> <span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</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;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">],</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</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="LC738" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Stat</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="819" style="width: 35px; color: rgba(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">@@ -819,14 +803,15 @@ int anker_rc(const HashMapCCI *template_index, unsigned char *qseq, int q_len, i</td>
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_start</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="c"> <span class="n" style="color: #333;">q_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="c"> <span class="n" style="color: #333;">q_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="c"> <span class="n" style="color: #333;">score_r</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="LC824" class="line" lang="c"> <span class="n" style="color: #333;">mem_count</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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825
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_start</span><span class="p">)</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="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_start</span><span class="p">;</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" 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;">q_start</span><span class="p">)</span> <span class="p">{</span></span>
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808
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_start</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="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">preseed</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">q_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_start</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="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="c"> <span class="n" style="color: #333;">score_r</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="LC813" class="line" lang="c"> <span class="n" style="color: #333;">mem_count</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="LC814" class="line" lang="c"> </span>
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</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;">q_end</span><span class="p">)</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="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">charpos</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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="993" style="width: 35px; color: rgba(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">@@ -993,6 +978,7 @@ int anker_rc_comp(const HashMapCCI *template_index, unsigned char *qseq, unsigne</td>
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993
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978
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<pre style="margin: 0;"> <span id="LC978" class="line" lang="c"> <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;">one2one</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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994
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979
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<pre style="margin: 0;"> <span id="LC979" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">score_r</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="n" style="color: #333;">prev</span><span class="p">;</span></span>
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995
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980
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<pre style="margin: 0;"> <span id="LC980" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">mem_count</span><span class="p">,</span> <span class="n" style="color: #333;">totMems</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Ns</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seeds</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">cPos</span><span class="p">,</span> <span class="n" style="color: #333;">iPos</span><span class="p">;</span></span>
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982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="c"> <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;">key</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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983
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<pre style="margin: 0;"> <span id="LC983" class="line" lang="c"> </span>
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984
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<pre style="margin: 0;"> <span id="LC984" 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;">template_index</span><span class="p">)</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">@@ -1026,14 +1012,22 @@ int anker_rc_comp(const HashMapCCI *template_index, unsigned char *qseq, unsigne</td>
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1026
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1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mem_count</span><span class="p">;</span></span>
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1027
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="c"> <span class="n" style="color: #333;">Ns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq_r_comp</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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1028
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1014
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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="c"> <span class="n" style="color: #333;">Ns</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Ns</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</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="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_start</span><span class="p">;</span></span>
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1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="c"> <span class="n" style="color: #333;">q_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_end</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="c"> <span class="n" style="color: #333;">q_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</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="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_start</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="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;">q_start</span><span class="p">)</span> <span class="p">{</span></span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_start</span><span class="p">;</span></span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">preseed</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">q_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_start</span><span class="p">);</span></span>
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1029
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="c"> <span class="p">}</span></span>
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1030
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1024
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="c"> <span class="n" style="color: #333;">score_r</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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1031
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1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="c"> <span class="n" style="color: #333;">mem_count</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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1032
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<pre style="margin: 0;">-<span id="LC1032" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span></span></span>
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1033
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<pre style="margin: 0;">-<span id="LC1033" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</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;">q_<span class="idiff left right">l</span>en</span><span class="p">)</span> <span class="p">{</span></span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="c"> </span>
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1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</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;">q_en<span class="idiff left right">d</span></span><span class="p">)</span> <span class="p">{</span></span>
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1034
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1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Ns</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</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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1035
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1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</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;">end</span><span class="p">)</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="c"> <span class="n" style="color: #333;"><span class="idiff left">key</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;">getKmer</span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">i</span></span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">);</span></span>
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1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="c"> <span class="n" style="color: #333;">getKmer<span class="idiff left">_macro</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cPos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">iPos</span></span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">);</span></span>
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1037
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1031
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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="c"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashMapCCI_get</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">);</span></span>
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1038
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1032
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<pre style="margin: 0;"> <span id="LC1032" class="line" lang="c"> </span>
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1039
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1033
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<pre style="margin: 0;"> <span id="LC1033" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">value</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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<a href="https://salsa.debian.org/med-team/kma/-/compare/3a0c2e0868ae672f84c60fafa3bcea1aa87ca059...97b5faf0bd92f7f493f9007ec81ec23752e9734e#6abbb3f721a6a2755259d4b75d5f59fbc6d160c1"><strong>align.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">@@ -22,6 +22,13 @@</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "hashmapcci.h"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "nw.h"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="nf" style="color: #900; font-weight: 600;">AlnScore</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">leadTailAlnPtr</span><span class="p">)(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <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;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="nf" style="color: #900; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trailTailAlnPtr</span><span class="p">)(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">AlnScore</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">skipLeadAln</span><span class="p">(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">leadTailAln</span><span class="p">(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">skipTrailAln</span><span class="p">(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">AlnScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Stat</span><span class="p">,</span> <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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">trailTailAln</span><span class="p">(</span><span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="n" style="color: #333;">AlnScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Stat</span><span class="p">,</span> <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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tseq</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</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;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">KMA</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_end</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Frag_align</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">KMA_score</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_end</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">preseed</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/3a0c2e0868ae672f84c60fafa3bcea1aa87ca059...97b5faf0bd92f7f493f9007ec81ec23752e9734e#596ab94993f840fb54df19a92f10da821eccfa7a"><strong>chain.c</strong></a>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdstat.h"</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chainSeedsPtr</span><span class="p">)(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</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="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chainSeeds</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trimSeedsPtr</span><span class="p">)(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</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;">trimSeeds</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">seedPoint_init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</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>
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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">@@ -78,7 +79,7 @@ void seedPoint_free(AlnPoints *src) {</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">chainSeeds</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</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;">mapQ</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">nMems</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">secondScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestPos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tStart</span><span class="p">,</span> <span class="n" style="color: #333;">tEnd</span><span class="p">,</span> <span class="n" style="color: #333;">qEnd</span><span class="p">,</span> <span class="n" style="color: #333;">tGap</span><span class="p">,</span> <span class="n" style="color: #333;">qGap</span><span class="p">,</span> <span class="n" style="color: #333;">nMin</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tStart</span><span class="p">,</span> <span class="n" style="color: #333;">tEnd</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">qStart</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">qEnd</span><span class="p">,</span> <span class="n" style="color: #333;">tGap</span><span class="p">,</span> <span class="n" style="color: #333;">qGap</span><span class="p">,</span> <span class="n" style="color: #333;">nMin</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rewards</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">@@ -87,29 +88,45 @@ int chainSeeds(AlnPoints *points, int q_len, int t_len, int kmersize, unsigned *</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">nMems</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nMems</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">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">bestPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">points</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">weight</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</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 right">M</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nMems</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">bestPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</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">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"> <span class="n" style="color: #333;">secondScore</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="LC94" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">bestScore</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</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="LC96" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</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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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> </span>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">)</span> <span class="p">{</span></span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</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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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"> <span class="n" style="color: #333;">tEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tEnd</span><span class="p">[</span><span class="n" style="color: #333;">i</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="c"> <span class="n" style="color: #333;">qEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">i</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="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tEnd</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">qEnd</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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" 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;">score</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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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</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="c"> </span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get stop score */</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tEnd</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">qEnd</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> </span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" 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;">gap</span><span class="p">)</span> <span class="p">{</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" 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;">gap</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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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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109
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">score</span></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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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">gap</span></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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111
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"> <span class="p">}</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> </span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</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="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="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"> <span class="p">}</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Ms</span><span class="p">);</span></span>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"> </span>
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114
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* 128 is the bandwidth */</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">nMin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">nMems</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;">128</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(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="211" style="width: 35px; color: rgba(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">@@ -194,6 +211,35 @@ int chainSeeds(AlnPoints *points, int q_len, int t_len, int kmersize, unsigned *</td>
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194
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="c"> <span class="p">}</span></span>
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195
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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196
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* penalize start */</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="c"> <span class="n" style="color: #333;">tStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="c"> <span class="n" style="color: #333;">qStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">tStart</span><span class="p">,</span> <span class="n" style="color: #333;">qStart</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap</span><span class="p">;</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="c"> </span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">gap</span><span class="p">)</span> <span class="p">{</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="224" 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">
224
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<pre style="margin: 0;">+<span id="LC224" 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;">gap</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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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">gap</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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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="c"> <span class="p">}</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="c"> </span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</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="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="236" 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">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="c"> <span class="p">}</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="241" 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">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update bestScore */</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bestPos</span><span class="p">)</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">@@ -201,29 +247,22 @@ int chainSeeds(AlnPoints *points, int q_len, int t_len, int kmersize, unsigned *</td>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"> <span class="n" style="color: #333;">bestPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC250" 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;">secondScore</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bestPos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="c"> <span class="n" style="color: #333;">secondScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate mapping quality */</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</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="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="mi" style="color: #099;">40</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="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secondScore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">bestScore</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">bestPos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">.</span><span class="mi" style="color: #099;">0</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;">bestScore</span><span class="p">)))</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="LC257" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span><span class="p">[</span><span class="n" style="color: #333;">bestPos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* penalize start */</span></span>
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<pre style="margin: 0;">-<span id="LC210" 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="LC211" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if(bestPos != 0) {</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> score = (MIN(points->qStart[bestPos], points->tStart[bestPos])) * pM;</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> bestScore += MAX(W1, score);</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if(points->qStart[0] == 0 && bestScore < points->score[0]) {</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> bestScore = points->score[0];</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> bestPos = 0;</span></span>
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<pre style="margin: 0;">-<span id="LC217" 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="LC218" 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="LC219" 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="LC259" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestPos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">chainSeeds_circular</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</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;">mapQ</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">nMems</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">secondScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestPos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tStart</span><span class="p">,</span> <span class="n" style="color: #333;">tEnd</span><span class="p">,</span> <span class="n" style="color: #333;">qEnd</span><span class="p">,</span> <span class="n" style="color: #333;">tGap</span><span class="p">,</span> <span class="n" style="color: #333;">qGap</span><span class="p">,</span> <span class="n" style="color: #333;">nMin</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tStart</span><span class="p">,</span> <span class="n" style="color: #333;">tEnd</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">qStart</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">qEnd</span><span class="p">,</span> <span class="n" style="color: #333;">tGap</span><span class="p">,</span> <span class="n" style="color: #333;">qGap</span><span class="p">,</span> <span class="n" style="color: #333;">nMin</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rewards</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">@@ -232,29 +271,45 @@ int chainSeeds_circular(AlnPoints *points, int q_len, int t_len, int kmersize, u</td>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c"> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c"> <span class="n" style="color: #333;">nMems</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nMems</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">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="c"> <span class="n" style="color: #333;">bestPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">points</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">weight</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</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 right">M</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nMems</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="c"> <span class="n" style="color: #333;">bestPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</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">1</span></span><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;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></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;">secondScore</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="LC239" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">bestScore</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</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="LC241" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</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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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</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="LC284" class="line" lang="c"> <span class="n" style="color: #333;">tEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tEnd</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="LC285" class="line" lang="c"> <span class="n" style="color: #333;">qEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</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="LC248" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tEnd</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">qEnd</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC252" 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;">score</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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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="c"> </span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get stop score */</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tEnd</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">qEnd</span><span class="p">);</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap</span><span class="p">;</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="c"> </span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" 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;">gap</span><span class="p">)</span> <span class="p">{</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="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;">gap</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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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="c"> <span class="n" style="color: #333;">gap</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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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="c"> <span class="p">}</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="c"> </span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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="LC305" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">score</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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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</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="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Ms</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* 128 is the bandwidth */</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"> <span class="n" style="color: #333;">nMin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">nMems</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;">128</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" style="width: 35px; color: rgba(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">@@ -390,6 +445,35 @@ int chainSeeds_circular(AlnPoints *points, int q_len, int t_len, int kmersize, u</td>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* penalize start */</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="c"> <span class="n" style="color: #333;">tStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</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="LC450" class="line" lang="c"> <span class="n" style="color: #333;">qStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</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="LC451" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">tStart</span><span class="p">,</span> <span class="n" style="color: #333;">qStart</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap</span><span class="p">;</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="c"> </span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">gap</span><span class="p">)</span> <span class="p">{</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" 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;">gap</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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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="c"> <span class="n" style="color: #333;">gap</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="LC462" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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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<pre style="margin: 0;">+<span id="LC467" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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="LC468" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</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="mi" style="color: #099;">0</span><span class="p">);</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update bestScore */</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bestPos</span><span class="p">)</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">@@ -397,22 +481,14 @@ int chainSeeds_circular(AlnPoints *points, int q_len, int t_len, int kmersize, u</td>
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="c"> <span class="n" style="color: #333;">bestPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC484" 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;">secondScore</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bestPos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="c"> <span class="n" style="color: #333;">secondScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate mapping quality */</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mapQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="mi" style="color: #099;">40</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="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secondScore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">bestScore</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">bestPos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">.</span><span class="mi" style="color: #099;">0</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;">bestScore</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* penalize start */</span></span>
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<pre style="margin: 0;">-<span id="LC406" 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="LC407" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if(bestPos != 0) {</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> score = (MIN(points->qStart[bestPos], points->tStart[bestPos])) * pM;</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> bestScore += MAX(W1, score);</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if(points->qStart[0] == 0 && bestScore < points->score[0]) {</span></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> bestScore = points->score[0];</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> bestPos = 0;</span></span>
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<pre style="margin: 0;">-<span id="LC413" 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="LC414" 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="LC415" 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="LC489" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate mapping quality */</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</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="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="mi" style="color: #099;">40</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="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">secondScore</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">bestScore</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">bestPos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">.</span><span class="mi" style="color: #099;">0</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;">bestScore</span><span class="p">))</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="LC491" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span><span class="p">[</span><span class="n" style="color: #333;">bestPos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestPos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="c"><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">@@ -430,8 +506,52 @@ void trimSeeds(AlnPoints *points, int start) {</td>
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<pre style="margin: 0;"> <span id="LC506" 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="LC507" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* iterate seeds on best chain */</span></span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="c"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim seed */</span></span>
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ts</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* ensure at least one nucleotide remains in seed */</span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</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;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ts</span><span class="p">;</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ts</span><span class="p">;</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]));</span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* iterate seeds on best chain */</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]))</span> <span class="p">{</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim seed */</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ts</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* ensure at least one nucleotide remains in seed */</span></span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</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;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ts</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ts</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">trimSeedsNoLead</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim the start of each seed */</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="c"> <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;">ts</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="LC544" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC546" 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;">points</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="c"> <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC548" 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="LC549" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">ts</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC550" 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="LC551" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* iterate seeds on best chain */</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left right">do</span></span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">while</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">start</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">points</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">next</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff right">]))</span></span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim seed */</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ts</span><span class="p">)</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">@@ -442,5 +562,5 @@ void trimSeeds(AlnPoints *points, int start) {</td>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ts</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ts</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="c"> <span class="p">}</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">while</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">start</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">points</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">next</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff right">]));</span></span></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/3a0c2e0868ae672f84c60fafa3bcea1aa87ca059...97b5faf0bd92f7f493f9007ec81ec23752e9734e#f966218212bf61b9bacc17a9bc23ef9ad756be7c"><strong>chain.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">@@ -38,6 +38,7 @@ struct alnPoints {</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* pointer to chaining method */</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="nf" style="color: #900; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chainSeedsPtr</span><span class="p">)(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</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="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="nf" style="color: #900; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trimSeedsPtr</span><span class="p">)(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* FUNCTIONS */</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">seedPoint_init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</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">@@ -46,3 +47,4 @@ void seedPoint_free(AlnPoints *src);</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">chainSeeds</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</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;">mapQ</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">chainSeeds_circular</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</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;">mapQ</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">trimSeeds</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">trimSeedsNoLead</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">kma (1.3.1<span class="idiff left right">5</span>-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kma (1.3.1<span class="idiff left right">7</span>-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * New upstream version 1.3.1<span class="idiff left right">5</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version 1.3.1<span class="idiff left right">7</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * d/p/blhc.patch: Propagate hardening flags to fix blhc</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Sat, 01 May 2021 22:20:10 +0530</span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/3a0c2e0868ae672f84c60fafa3bcea1aa87ca059...97b5faf0bd92f7f493f9007ec81ec23752e9734e#5bb411548ec4b39482e6de83d3ad98f29b1162b1"><strong>kma.c</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">@@ -97,89 +97,109 @@ char * strjoin(char **strings, int len) {</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">newStr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"><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;">helpMessage</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exeStatus</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">helpOut</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">exeStatus</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="LC103" class="line" lang="c"> <span class="n" style="color: #333;">helpOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stdout</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">helpOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stderr</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"# KMA-%s mapps raw reads to a template database.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">KMA_VERSION</span><span class="p">);</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Options are:</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Desc:</span><span class="se" style="color: #d14;">\t\t\t\t</span><span class="s" style="color: #d14;">Default:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Requirements:</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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109
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC109" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</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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<td class="old_line diff-line-num old" data-linenumber="110" 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">
110
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC110" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-o</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Output file</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">None</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">REQUIRED</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="old_line diff-line-num old" data-linenumber="111" 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">
111
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC111" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-t_db</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Template DB</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">None</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">REQUIRED</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="old_line diff-line-num old" data-linenumber="112" 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">
112
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC112" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-i</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Input file name(s)</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">STDIN</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="old_line diff-line-num old" data-linenumber="113" 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">
113
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC113" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ipe</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Input paired end file name(s)</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="old_line diff-line-num old" data-linenumber="114" 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">
114
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC114" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-int</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Input interleaved file name(s)</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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115
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC115" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-k</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Kmersize</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"DB defined"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="116" 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">
116
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC116" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ts</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Trim front of seeds with ts</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="117" 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">
117
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC117" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ml</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum alignment length</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="118" 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">
118
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC118" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-p</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">p-value</span><span class="se" style="color: #d14;">\t\t\t\t</span><span class="s" style="color: #d14;">0.05</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="old_line diff-line-num old" data-linenumber="119" 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">
119
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC119" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ConClave</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ConClave version</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">1</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="old_line diff-line-num old" data-linenumber="120" 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">
120
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC120" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-mem_mode</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Use kmers to choose best</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">template, and save memory</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False</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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121
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC121" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-proxi</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Use proximity scoring under</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">template mapping</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False/1.0</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="old_line diff-line-num old" data-linenumber="122" 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">
122
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC122" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ex_mode</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Searh kmers exhaustively</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False</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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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ef</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Print additional features</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="124" 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">
124
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC124" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-vcf</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Make vcf file, 2 to apply FT</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False/0</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="old_line diff-line-num old" data-linenumber="125" 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">
125
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC125" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-sam</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Output sam to stdout, 4 to </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">only output mapped reads, </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">2096 for aligned</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False/0</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="old_line diff-line-num old" data-linenumber="126" 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">
126
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC126" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-nc</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">No consensus file</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="127" 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">
127
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC127" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-na</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">No aln file</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="128" 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">
128
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC128" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-nf</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">No frag file</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="129" 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">
129
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC129" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-deCon</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Remove contamination</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="130" 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">
130
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC130" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-dense</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Do not allow insertions</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">in assembly</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="131" 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">
131
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC131" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-sasm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Skip alignment and assembly</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="132" 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">
132
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC132" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ref_fsa</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Consensus sequnce will</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">have </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">n</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> instead of gaps</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False / 0</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="old_line diff-line-num old" data-linenumber="133" 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">
133
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC133" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-matrix</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Print assembly matrix</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="134" 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">
134
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC134" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-a</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Print all best mappings</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="135" 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">
135
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC135" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-mp</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum phred score</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">20</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="old_line diff-line-num old" data-linenumber="136" 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">
136
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC136" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-eq</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum avg. quality score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</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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137
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC137" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-5p</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Cut a constant number of</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">nucleotides from the 5 prime.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</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="old_line diff-line-num old" data-linenumber="138" 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">
138
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC138" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-3p</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Cut a constant number of</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">nucleotides from the 3 prime.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</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="old_line diff-line-num old" data-linenumber="139" 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">
139
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC139" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-Sparse</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Only count kmers</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="140" 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">
140
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC140" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-Mt1</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Map only to </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">num</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> template.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0 / False</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="old_line diff-line-num old" data-linenumber="141" 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">
141
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC141" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ID</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum ID</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">1.0%%</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="old_line diff-line-num old" data-linenumber="142" 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">
142
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC142" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ss</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Sparse sorting (q,c,d)</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">q</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="old_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
143
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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-pm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Pairing method (p,u,f)</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">u</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="old_line diff-line-num old" data-linenumber="144" 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">
144
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC144" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-fpm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Fine Pairing method (p,u,f)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">u</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="old_line diff-line-num old" data-linenumber="145" 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">
145
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC145" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-apm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Sets both pm and fpm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">u</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="old_line diff-line-num old" data-linenumber="146" 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">
146
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC146" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-shm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Use shared DB made by kma_shm</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0 (lvl)</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="old_line diff-line-num old" data-linenumber="147" 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">
147
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC147" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-mmap</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Memory map *.comp.by</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="old_line diff-line-num old" data-linenumber="148" 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">
148
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC148" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-tmp</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Set directory for temporary files.</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="old_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
149
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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-1t1</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Force end to end mapping</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="150" 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">
150
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC150" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-hmm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Use a HMM to assign template(s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">to query sequences</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">True</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="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
151
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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ck</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Count kmers instead of</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">pseudo alignment</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-ca</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Make circular alignments</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="153" 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">
153
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC153" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-boot</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Bootstrap sequence</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="154" 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">
154
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC154" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-bc</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Base calls should be</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">significantly overrepresented.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">[True]</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="old_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
155
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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-bc90</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Base calls should be both</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">significantly overrepresented,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">and have 90%% agreement.</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="156" 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">
156
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC156" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-bcNano</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Call bases at suspicious</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">deletions, made for nanopore.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
157
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC157" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-bcd</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum depth at base</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">1</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="old_line diff-line-num old" data-linenumber="158" 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">
158
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC158" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-bcg</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Maintain insignificant gaps</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="old_line diff-line-num old" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC159" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-and</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Both mrs and p_value thresholds</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">has to reached to in order to</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">report a template hit.</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">or</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="old_line diff-line-num old" data-linenumber="160" 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">
160
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC160" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-oa</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Output all, disregard mrs and p-value</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">when reporting a template hit</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
161
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC161" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-mq</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum mapping quality</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">0</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="old_line diff-line-num old" data-linenumber="162" 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">
162
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC162" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-mrs</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum alignment score,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">normalized to alignment length</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0.50</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="old_line diff-line-num old" data-linenumber="163" 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">
163
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC163" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-mrc</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum read coverage</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">0.10</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="old_line diff-line-num old" data-linenumber="164" 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">
164
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC164" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-mct</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Max overlap between templates</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0.10</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="old_line diff-line-num old" data-linenumber="165" 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">
165
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC165" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-reward</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Score for match</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">1</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="old_line diff-line-num old" data-linenumber="166" 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">
166
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC166" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-penalty</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for mismatch</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">-2</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="old_line diff-line-num old" data-linenumber="167" 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">
167
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC167" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-gapopen</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for gap opening</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">-3</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="old_line diff-line-num old" data-linenumber="168" 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">
168
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC168" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-gapextend</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for gap extension</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-1</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="old_line diff-line-num old" data-linenumber="169" 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">
169
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC169" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-per</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Reward for pairing reads</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7</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="old_line diff-line-num old" data-linenumber="170" 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">
170
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC170" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-localopen</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for openning a local chain</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-6</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="old_line diff-line-num old" data-linenumber="171" 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">
171
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC171" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-Npenalty</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty matching N</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">0</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="old_line diff-line-num old" data-linenumber="172" 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">
172
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC172" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-transition</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for transition</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">-2</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="old_line diff-line-num old" data-linenumber="173" 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">
173
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC173" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-transversion</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for transversion</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-2</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="old_line diff-line-num old" data-linenumber="174" 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">
174
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC174" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-cge</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Set CGE penalties and rewards</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False</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="old_line diff-line-num old" data-linenumber="175" 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">
175
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC175" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-t</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Number of threads</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">1</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="old_line diff-line-num old" data-linenumber="176" 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">
176
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC176" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-status</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Extra status</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="old_line diff-line-num old" data-linenumber="177" 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">
177
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC177" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-verbose</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Extra verbose</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="old_line diff-line-num old" data-linenumber="178" 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">
178
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC178" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-c</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Citation</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="old_line diff-line-num old" data-linenumber="179" 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">
179
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC179" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-v</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Version</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="old_line diff-line-num old" data-linenumber="180" 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">
180
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC180" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</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;">-h</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Shows this help message</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="old_line diff-line-num old" data-linenumber="181" 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">
181
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC181" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</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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<td class="old_line diff-line-num old" data-linenumber="182" 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">
182
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<td class="new_line diff-line-num old" data-linenumber="100" 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="LC182" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">exeStatus</span><span class="p">);</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"><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;">helpMessage</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exitStatus</span><span class="p">)</span> <span class="p">{</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> </span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</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;">exitStatus</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">stdout</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="c"> </span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# KMA-%s maps and/or aligns raw reads to a template database.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">KMA_VERSION</span><span class="p">);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> </span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Options:"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Desc:"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Default:"</span><span class="p">);</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> </span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># Input:</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="new_line diff-line-num new" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-i"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Single end input(s)"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stdin"</span><span class="p">);</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ipe"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Paired end input(s)"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-int"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Interleaved input(s)"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> </span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># Output:</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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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output prefix"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ef"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output additional features"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-vcf"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output vcf file, 2 to apply FT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-sam"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output sam, 4/2096 for mapped/aligned"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="118" 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">
118
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nc"</span><span class="p">,</span> <span class="s" style="color: #d14;">"No consensus file"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nc"</span><span class="p">,</span> <span class="s" style="color: #d14;">"No aln file"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="120" 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">
120
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nf"</span><span class="p">,</span> <span class="s" style="color: #d14;">"No frag file"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="121" 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">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-matrix"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output assembly matrix"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output all template mappings"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="123" 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">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-and"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Use both mrs and p-value on consensus"</span><span class="p">,</span> <span class="s" style="color: #d14;">"or"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-oa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Use neither mrs or p-value on consensus"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> </span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># Consensus:</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="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-bc"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum support to call bases"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-bcNano"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Altered indel calling for ONT data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="129" 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">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-bcd"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum depth to cal bases"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="130" 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">
130
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-bcg"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Maintain insignificant gaps"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="131" 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">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ID"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum consensus ID"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.0%"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-dense"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Skip insertion in consensus"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ref_fsa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Use n's on indels"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="134" 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">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> </span>
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<td class="new_line diff-line-num new" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># General:</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="new_line diff-line-num new" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-t_db"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Template DB"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-p"</span><span class="p">,</span> <span class="s" style="color: #d14;">"P-value"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0.05"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-shm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Use DB in shared memory"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="139" 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">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-mmap"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Memory map *.comp.b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-tmp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Set directory for temporary files"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-t"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number of threads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-status"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Extra status"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-verbose"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Extra verbose"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Citation"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-v"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Version"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="146" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-h"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Shows this help message"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> </span>
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<td class="new_line diff-line-num new" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># Template mapping:</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="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ConClave"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ConClave version"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-mem_mode"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Base ConClave on template mappings"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-proxi"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Proximity scoring (negative for soft)"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False/1.0"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ex_mode"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Searh kmers exhaustively"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-deCon"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Remove contamination"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-Sparse"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Only count kmers"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="155" 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">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ss"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Sparse sorting (q,c,d)"</span><span class="p">,</span> <span class="s" style="color: #d14;">"q"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-Mt1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Map everything to one template"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False/0"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-pm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Pairing method (p,u,f)"</span><span class="p">,</span> <span class="s" style="color: #d14;">"u"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="183" 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="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-1t1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"One query to one template"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-hmm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Use a HMM to assign template(s)"</span><span class="p">,</span> <span class="s" style="color: #d14;">"True"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="160" 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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ck"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Count k-mers over pseudo alignment"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</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="c"> </span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># Chaining:</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="new_line diff-line-num new" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-k"</span><span class="p">,</span> <span class="s" style="color: #d14;">"K-mersize"</span><span class="p">,</span> <span class="s" style="color: #d14;">"DB defined"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ts"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim front of seeds"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ssa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Seeds soround alignments"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ex_mode"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Searh kmers exhaustively"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-fpm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Pairing method (p,u,f)"</span><span class="p">,</span> <span class="s" style="color: #d14;">"u"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-mq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum mapping quality"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"> </span>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># Alignment:</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="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ca"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Circular alignments"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-mrs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum relative alignment score"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0.5"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-mrc"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum query coverage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0.0"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ml"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum alignment length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"16"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-reward"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Score for match"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-penalty"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Penalty for mismatch"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-gapopen"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Penalty for gap opening"</span><span class="p">,</span> <span class="s" style="color: #d14;">"3"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-gapextend"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Penalty for gap extension"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-per"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Reward for pairing reads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"7"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-Npenalty"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Penalty matching N"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-transition"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Penalty for transition"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-transversion"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Penalty for transversion"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-sasm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Skip alignment"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="c"> </span>
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<td class="new_line diff-line-num new" 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="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># Trimming:</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="new_line diff-line-num new" 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="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-mp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum phred score"</span><span class="p">,</span> <span class="s" style="color: #d14;">"20"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-eq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum avg. quality score"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="188" 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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-5p"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim 5 prime"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="189" 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">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-3p"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim 3 prime"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="190" 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">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-ml"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"16"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="191" 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">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-xl"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Maximum length on se"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2147483647"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="192" 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">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-boot"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Bootstrap sub-sequence"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"> </span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># Presets:</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="new_line diff-line-num new" data-linenumber="195" 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">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-apm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Sets both pm and fpm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"u"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="196" 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">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-cge"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Set CGE penalties and rewards"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="197" 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">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-mint2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Set 2ng gen Mintyper preset"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-mint3"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Set 3rd gen Mintyper preset"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="c"> </span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</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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<td class="new_line diff-line-num new" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="c"> </span>
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<td class="new_line diff-line-num new" data-linenumber="202" 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">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">exitStatus</span><span class="p">);</span></span>
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183
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c"><span class="p">}</span></span>
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184
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"></span>
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185
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<td class="new_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">kma_main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</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="205" style="width: 35px; color: rgba(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="225" style="width: 35px; color: rgba(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">@@ -205,7 +225,7 @@ int kma_main(int argc, char *argv[]) {</td>
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205
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"> <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;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_PE</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_INT</span><span class="p">,</span> <span class="n" style="color: #333;">Ts</span><span class="p">,</span> <span class="n" style="color: #333;">Tv</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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206
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"> <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;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">spltDB</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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207
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"> <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;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">one2one</span><span class="p">;</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="c"> <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;">sparse_run</span><span class="p">,</span> <span class="n" style="color: #333;">ts</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">status</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="new_line diff-line-num new" data-linenumber="228" 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">
228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="c"> <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;">sparse_run</span><span class="p">,</span> <span class="n" style="color: #333;">ts</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">maxlen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">status</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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<td class="new_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="c"> <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;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">;</span></span>
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210
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">;</span></span>
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211
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<td class="new_line diff-line-num" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles_PE</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles_INT</span><span class="p">,</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="275" style="width: 35px; color: rgba(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">@@ -255,6 +275,7 @@ int kma_main(int argc, char *argv[]) {</td>
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255
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="c"> <span class="n" style="color: #333;">kmersize</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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256
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="c"> <span class="n" style="color: #333;">ts</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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257
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="c"> <span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c"> <span class="n" style="color: #333;">maxlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2147483647</span><span class="p">;</span></span>
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258
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<td class="new_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"> <span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">;</span></span>
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259
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c"> <span class="n" style="color: #333;">support</span> <span class="o" style="font-weight: 600;">=</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>
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260
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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;">minFrac</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="516" style="width: 35px; color: rgba(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="537" style="width: 35px; color: rgba(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">@@ -516,6 +537,10 @@ int kma_main(int argc, char *argv[]) {</td>
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516
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537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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517
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="c"> <span class="p">}</span></span>
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518
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="540" 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">
540
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<pre style="margin: 0;">+<span id="LC540" 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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-ssa"</span><span class="p">)</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="LC541" class="line" lang="c"> <span class="n" style="color: #333;">trimSeedsPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">trimSeedsNoLead</span><span class="p">;</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="c"> <span class="n" style="color: #333;">leadTailAlnPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">skipLeadAln</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="c"> <span class="n" style="color: #333;">trailTailAlnPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">skipTrailAln</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC544" 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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-ml"</span><span class="p">)</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="LC545" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</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">@@ -525,6 +550,15 @@ int kma_main(int argc, char *argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="c"> <span class="p">}</span></span>
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC553" 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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-xl"</span><span class="p">)</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="LC554" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="c"> <span class="n" style="color: #333;">maxlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtoul</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC557" 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;">exeBasic</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="LC558" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Invalid minimum length parsed</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="LC559" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC562" 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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-mp"</span><span class="p">)</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="LC563" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span><span class="p">;</span></span>
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530
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</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="984" style="width: 35px; color: rgba(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="1018" style="width: 35px; color: rgba(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">@@ -984,7 +1018,7 @@ int kma_main(int argc, char *argv[]) {</td>
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984
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1018
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<pre style="margin: 0;"> <span id="LC1018" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span><span class="p">;</span></span>
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985
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1019
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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="c"> <span class="p">}</span></span>
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986
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1020
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<pre style="margin: 0;"> <span id="LC1020" class="line" lang="c"> <span class="n" style="color: #333;">preseed</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;">exhaustive</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="987" 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">
987
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<td class="new_line diff-line-num old" data-linenumber="1021" 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="LC987" class="line" lang="c"> <span class="n" style="color: #333;">trimSeeds</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">ts</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1021" 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">
1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="c"> <span class="n" style="color: #333;">trimSeeds<span class="idiff left right">Ptr</span></span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">ts</span><span class="p">);</span></span>
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988
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1022
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
989
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">kmaPipe</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmaPipeThread</span><span class="p">)</span> <span class="p">{</span></span>
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990
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1024
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-sam</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> and </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-status</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> cannot coincide.</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="1272" style="width: 35px; color: rgba(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="1306" style="width: 35px; color: rgba(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">@@ -1272,7 +1306,7 @@ int kma_main(int argc, char *argv[]) {</td>
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1272
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1306
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="c"> </span>
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1273
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<td class="new_line diff-line-num" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* SE */</span></span>
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<td class="old_line diff-line-num" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1274
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<td class="new_line diff-line-num" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1308
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<pre style="margin: 0;"> <span id="LC1308" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fileCounter</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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<td class="old_line diff-line-num old" data-linenumber="1275" 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">
1275
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<td class="new_line diff-line-num old" data-linenumber="1309" 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="LC1275" class="line" lang="c"> <span class="n" style="color: #333;">totFrags</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">run_input</span><span class="p">(</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">minQ</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;">threeClip</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="n" style="color: #333;">ioStream</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1276" 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="new_line diff-line-num new" data-linenumber="1309" 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">
1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="c"> <span class="n" style="color: #333;">totFrags</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">run_input</span><span class="p">(</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">minQ</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;">threeClip</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">maxlen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="n" style="color: #333;">ioStream</span><span class="p">);</span></span>
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1276
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1310
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<pre style="margin: 0;"> <span id="LC1310" class="line" lang="c"> <span class="p">}</span></span>
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1277
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1311
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<pre style="margin: 0;"> <span id="LC1311" class="line" lang="c"> </span>
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1278
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<td class="new_line diff-line-num" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1312
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* PE */</span></span>
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<li id="97e3379ce2e33418ea5b83d3faaf35326b973d41">
<a href="https://salsa.debian.org/med-team/kma/-/compare/3a0c2e0868ae672f84c60fafa3bcea1aa87ca059...97b5faf0bd92f7f493f9007ec81ec23752e9734e#97e3379ce2e33418ea5b83d3faaf35326b973d41"><strong>nw.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,9 +23,9 @@</td>
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23
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "pherror.h"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdnuc.h"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">NW</span><span class="p">(</span><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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queryOrg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">NW</span><span class="p">(</span><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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queryOrg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</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">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">template_length</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="n" style="color: #333;">thisScore</span><span class="p">,</span> <span class="n" style="color: #333;">nuc_pos</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">template_length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="n" style="color: #333;">thisScore</span><span class="p">,</span> <span class="n" style="color: #333;">nuc_pos</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">[</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;">D_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">D_prev</span><span class="p">,</span> <span class="n" style="color: #333;">Q</span><span class="p">,</span> <span class="n" style="color: #333;">Q_prev</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">P_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">P_prev</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">t_nuc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">E</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">E_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">e</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;">AlnScore</span> <span class="n" style="color: #333;">Stat</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">@@ -40,9 +40,8 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</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="LC42" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</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="LC43" class="line" lang="c"> <span class="n" style="color: #333;">template_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</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="LC45" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left">aligned</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">pos</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left right">template_length</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">query</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="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">queryOrg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</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">@@ -308,9 +307,9 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Stat</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">NW_band</span><span class="p">(</span><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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queryOrg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">NW_band</span><span class="p">(</span><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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queryOrg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</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">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">template_length</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="n" style="color: #333;">thisScore</span><span class="p">,</span> <span class="n" style="color: #333;">nuc_pos</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">template_length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">pos</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="n" style="color: #333;">thisScore</span><span class="p">,</span> <span class="n" style="color: #333;">nuc_pos</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bq_len</span><span class="p">,</span> <span class="n" style="color: #333;">halfBand</span><span class="p">,</span> <span class="n" style="color: #333;">sn</span><span class="p">,</span> <span class="n" style="color: #333;">en</span><span class="p">,</span> <span class="n" style="color: #333;">sq</span><span class="p">,</span> <span class="n" style="color: #333;">eq</span><span class="p">,</span> <span class="n" style="color: #333;">q_pos</span><span class="p">,</span> <span class="n" style="color: #333;">c_pos</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">D_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">D_prev</span><span class="p">,</span> <span class="n" style="color: #333;">Q</span><span class="p">,</span> <span class="n" style="color: #333;">Q_prev</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">P_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">P_prev</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">t_nuc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">E</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">E_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">e</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">@@ -326,7 +325,6 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t_s</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</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="LC327" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</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="LC329" class="line" lang="c"> <span class="n" style="color: #333;">template_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</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;">t_len</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="LC329" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">template_length</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="c"> <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">@@ -56,7 +56,7 @@ struct aln {</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define NWLOAD 1</span></span>
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<pre style="margin: 0;"> <span id="LC57" 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="LC58" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">NW</span><span class="p">(</span><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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queryOrg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</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;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">NW_band</span><span class="p">(</span><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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queryOrg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">NW</span><span class="p">(</span><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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queryOrg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</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">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">template_length</span></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;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">NW_band</span><span class="p">(</span><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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queryOrg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</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">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">template_length</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">NW_score</span><span class="p">(</span><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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queryOrg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template_length</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"><span class="n" style="color: #333;">AlnScore</span> <span class="nf" style="color: #900; font-weight: 600;">NW_band_score</span><span class="p">(</span><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;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queryOrg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template_length</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">@@ -29,7 +29,7 @@</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">printFsa_ptr</span><span class="p">)(</span><span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</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;">printFsa</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">printFsa_pair_ptr</span><span class="p">)(</span><span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</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;">printFsa_pair</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minQ</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threeClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trans</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minQ</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threeClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxlen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trans</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">phredScale</span><span class="p">,</span> <span class="n" style="color: #333;">phredCut</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">FASTQ</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">@@ -65,55 +65,59 @@ long unsigned run_input(char **inputfiles, int fileCount, int minPhred, int minQ</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* parse reads */</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">FileBuffgetFq</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">trans</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim */</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</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;">threeClip</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</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;">phredCut</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">phredCut</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC80" 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="LC81" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> for(i = start; i < end; ++i) {</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if(seq[i] < phredCut) {</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> seq[i] = 4;</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxlen</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim */</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">;</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</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;">threeClip</span><span class="p">;</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</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;">phredCut</span><span class="p">)</span> <span class="p">{</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="p">}</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">phredCut</span><span class="p">)</span> <span class="p">{</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"> <span class="p">}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> for(i = start; i < end; ++i) {</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if(seq[i] < phredCut) {</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> seq[i] = 4;</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* print */</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">minQ</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">eQual</span><span class="p">(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">minQ</span><span class="p">,</span> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">phredScale</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump seq */</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">printFsa_ptr</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC85" 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="LC86" 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="LC87" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* print */</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">minQ</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">eQual</span><span class="p">(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">minQ</span><span class="p">,</span> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">phredScale</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump seq */</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">printFsa_ptr</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC99" 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;">FASTQ</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">FileBuffgetFsa</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">trans</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* remove leading and trailing N's */</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"> <span class="n" style="color: #333;">start</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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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</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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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</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="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</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="mi" style="color: #099;">4</span><span class="p">)</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="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> <span class="p">}</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"> <span class="p">}</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minlen</span><span class="p">)</span> <span class="p">{</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump seq */</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">printFsa_ptr</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxlen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* remove leading and trailing N's */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">start</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="new_line diff-line-num new" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</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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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</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="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="p">}</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="p">}</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minlen</span><span class="p">)</span> <span class="p">{</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump seq */</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">printFsa_ptr</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> <span class="p">}</span></span>
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117
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="p">}</span></span>
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118
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> <span class="p">}</span></span>
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/3a0c2e0868ae672f84c60fafa3bcea1aa87ca059...97b5faf0bd92f7f493f9007ec81ec23752e9734e#04f591434765972061a4501d514d48d8e013bc2a"><strong>runinput.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">@@ -23,7 +23,7 @@</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* pointers determining how to deliver the input */</span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="nf" style="color: #900; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">printFsa_ptr</span><span class="p">)(</span><span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="nf" style="color: #900; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">printFsa_pair_ptr</span><span class="p">)(</span><span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minQ</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threeClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trans</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</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="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minQ</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threeClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxlen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trans</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</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="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_PE</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minQ</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threeClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trans</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</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="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_INT</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minQ</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threeClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trans</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</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="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">bootFsa</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</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="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define setEx(src, pos)(src[pos >> 3] |= (1 << (pos & 7)))</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define unsetEx(src, pos)(src[pos >> 3] ^= (1 << (pos & 7)))</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define getEx(src, pos)((src[pos >> 3] >> (pos & 7)) & 1)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define getKmer_macro(kmer, Comp, pos, cPos, iPos, shifter) \</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> iPos = (pos & 31) << 1;\</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> cPos = pos >> 5;\</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> kmer = (iPos <= shifter) ? ((Comp[cPos] << iPos) >> shifter) : (((Comp[cPos] << iPos) | (Comp[cPos + 1] >> (64-iPos))) >> shifter);</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">getKmer</span><span class="p">(</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">cPos</span><span class="p">,</span> <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;">shifter</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">makeKmer</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/3a0c2e0868ae672f84c60fafa3bcea1aa87ca059...97b5faf0bd92f7f493f9007ec81ec23752e9734e#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4"><strong>version.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">@@ -17,4 +17,4 @@</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC18" 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="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.1<span class="idiff left right">5</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.1<span class="idiff left right">7</span>"</span></span></pre>
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