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<h3>
Nilesh Patra pushed to branch upstream
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/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f">e82ae7fe</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-01-22T16:48:05+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.28</pre>
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<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#302e1fff50e6c455134afebd2f2fa2f0c5b717d8">
alnfrags.c
</a>
</li>
<li class="file-stats">
<a href="#6f01b21e666698a62c6dd6fcadb36a64d4bc30d4">
frags.c
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<li class="file-stats">
<a href="#7eed163ea0757dada23cd667898abf840233da45">
index.c
</a>
</li>
<li class="file-stats">
<a href="#7a122ded91580b81c8f6685ec7894f7fe4da3564">
qualcheck.c
</a>
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<li class="file-stats">
<a href="#ca9efd475143efe0a1b0464c67f49900d98ca75a">
runkma.c
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<li class="file-stats">
<a href="#7d21f6d2a4876afc9692035ab8b768c7552662bb">
seqparse.c
</a>
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<li class="file-stats">
<a href="#f80652dda49a7117428c0f92935664fc8cd4e2d1">
spltdb.c
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<li class="file-stats">
<a href="#05f0af3a59c658f981844c8774c273c9b6448703">
stdstat.c
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<li class="file-stats">
<a href="#54798841eb38daaad8bb0e117d6d873232389f69">
stdstat.h
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<li class="file-stats">
<a href="#1c6375d34d9e418d1139bd146337fb256ac24a2a">
tmp.c
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<li class="file-stats">
<a href="#f568890dac40d04b36ce5786c44ac5704d31fe78">
updateindex.c
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<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/kma/README.html)</span>
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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Getting Started #</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="p">```</span></span>
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<li id="302e1fff50e6c455134afebd2f2fa2f0c5b717d8">
<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#302e1fff50e6c455134afebd2f2fa2f0c5b717d8"><strong>alnfrags.c</strong></a>
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<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1140" style="width: 35px; color: rgba(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="1140" style="width: 35px; color: rgba(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">@@ -1140,7 +1140,7 @@ void * alnFrags_threaded(void * arg) {</td>
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<td class="old_line diff-line-num" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1140
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<td class="new_line diff-line-num" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1140
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1140" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1141
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<td class="new_line diff-line-num" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1141
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1141" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1142
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<td class="new_line diff-line-num" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1142
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1142" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump seq to all */</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1143" 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">
1143
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<td class="new_line diff-line-num old" data-linenumber="1143" 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="LC1143" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">frag_out_all</span><span class="idiff left"> </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">unmapped</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1144" 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="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">frag_out_all</span><span class="p">)</span> <span class="p">{</span></span>
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1144
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1144
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">unmapped</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="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" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1145
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<td class="new_line diff-line-num" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="c"> <span class="n" style="color: #333;">updateAllFrag</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;">seq</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matched_templates</span><span class="p">,</span> <span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_all</span><span class="p">);</span></span>
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1146
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1146
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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</li>
<li id="6f01b21e666698a62c6dd6fcadb36a64d4bc30d4">
<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#6f01b21e666698a62c6dd6fcadb36a64d4bc30d4"><strong>frags.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="69" style="width: 35px; color: rgba(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="69" style="width: 35px; color: rgba(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">@@ -69,6 +69,10 @@ void updateAllFrag(unsigned char *qseq, int q_len, int bestHits, int best_read_s</td>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <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;">update</span><span class="p">;</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACGTN-"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC72" 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;">q_len</span><span class="p">)</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;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">check</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="LC78" class="line" lang="c"> <span class="n" style="color: #333;">avail</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bytes</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">@@ -157,7 +161,13 @@ void updateAllFrag(unsigned char *qseq, int q_len, int bestHits, int best_read_s</td>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">check</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</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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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* q-bound */</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">header</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;">header</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;">header</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;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><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="mi" style="color: #099;">1</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="LC166" 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;">header</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;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC167" 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="LC168" 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;">header</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="LC169" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</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="LC171" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">avail</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">check</span><span class="p">)</span> <span class="p">{</span></span>
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162
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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;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">avail</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="n" style="color: #333;">writeGzFileBuff</span><span class="p">(</span><span class="n" style="color: #333;">dest</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">@@ -165,9 +175,9 @@ void updateAllFrag(unsigned char *qseq, int q_len, int bestHits, int best_read_s</td>
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165
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</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="p">)</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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166
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="p">}</span></span>
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167
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">update</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\t'</span><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 class="n" style="color: #333;"><span class="idiff left">header</span></span><span class="o" style="font-weight: 600;"><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="n" style="color: #333;"><span class="idiff">header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">len</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">1</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="sc" style="color: #d14;"><span class="idiff right">'\n'</span></span><span class="p">;</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">memcpy</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">update</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header</span></span><span class="o" style="font-weight: 600;"><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">header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">len</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">update</span><span class="idiff left"> </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">header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">len</span></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="n" style="color: #333;"><span class="idiff left">memcpy</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">update</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header</span></span><span class="o" style="font-weight: 600;"><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">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">--</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">update</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">i</span></span><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 class="idiff left">*</span></span><span class="n" style="color: #333;">update</span><span class="o" style="font-weight: 600;"><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="sc" style="color: #d14;"><span class="idiff right">'\n'</span></span><span class="p">;</span></span>
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171
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="c"> </span>
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172
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">avail</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">check</span><span class="p">;</span></span>
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173
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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;">update</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#7eed163ea0757dada23cd667898abf840233da45"><strong>index.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -92,7 +92,8 @@ int index_main(int argc, char *argv[]) {</td>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" 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;">"# Too few arguments handed.</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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93
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">helpMessage</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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94
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94
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<pre style="margin: 0;"> <span id="LC94" 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="k" style="font-weight: 600;">sizeof</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="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">8</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="n" style="color: #333;">ERROR</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="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;">"Need a 64-bit system.</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="LC96" 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="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>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* set defaults */</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#7a122ded91580b81c8f6685ec7894f7fe4da3564"><strong>qualcheck.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">@@ -44,6 +44,7 @@ int lengthCheck(HashMap *templates, CompDNA *qseq, int MinKlen, double homQ, dou</td>
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<pre style="margin: 0;"> <span id="LC44" 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;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">templates</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 class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MinKlen</span><span class="p">)</span> <span class="p">{</span></span>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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46
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46
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<pre style="margin: 0;"> <span id="LC46" 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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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">comp_rc</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#ca9efd475143efe0a1b0464c67f49900d98ca75a"><strong>runkma.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">@@ -933,7 +933,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="c"> <span class="p">}</span></span>
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="c"> </span>
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tot</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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936
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<pre style="margin: 0;">-<span id="LC936" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left">-</span></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="LC936" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplate</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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937
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<pre style="margin: 0;"> <span id="LC937" class="line" lang="c"> <span class="n" style="color: #333;">best_read_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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938
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<pre style="margin: 0;"> <span id="LC938" class="line" lang="c"> <span class="n" style="color: #333;">bestNum</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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939
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939
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<pre style="margin: 0;"> <span id="LC939" 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">@@ -1000,38 +1000,14 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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1000
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="c"> <span class="n" style="color: #333;">strrc</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;">seq</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>
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1002
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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="c"> <span class="p">}</span></span>
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1003
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="c"> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read_score</span><span class="p">;</span></span>
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1004
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fragmentCounts</span><span class="p">)</span> <span class="p">{</span></span>
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1005
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<pre style="margin: 0;">-<span id="LC1005" class="line" lang="c"> <span class="n" style="color: #333;">fragmentCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1006
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="c"> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="c"> <span class="p">}</span></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="c"> </span>
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1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump frag info */</span></span>
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1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Frag</span><span class="p">));</span></span>
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1011
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<pre style="margin: 0;">-<span id="LC1011" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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;">qseq</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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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</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;">bestHits</span><span class="p">;</span></span>
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1013
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<pre style="margin: 0;">-<span id="LC1013" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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="p">(</span><span class="n" style="color: #333;">sparse</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">read_score</span><span class="p">;</span></span>
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1014
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</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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1015
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<pre style="margin: 0;">-<span id="LC1015" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</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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1016
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<pre style="margin: 0;">-<span id="LC1016" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</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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1017
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<pre style="margin: 0;">-<span id="LC1017" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flag</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;">alignFrag</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;">ustrdup</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;">seq</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>
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1019
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<pre style="margin: 0;">-<span id="LC1019" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ustrdup</span><span class="p">(</span><span class="n" style="color: #333;">header</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;">header</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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1020
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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">];</span></span>
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<td class="old_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">
1021
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<pre style="margin: 0;">-<span id="LC1021" class="line" lang="c"> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrag</span><span class="p">;</span></span>
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1022
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<td class="new_line diff-line-num old" data-linenumber="1003" 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="LC1022" class="line" lang="c"> </span>
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1023
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<pre style="margin: 0;">-<span id="LC1023" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">fragCount</span><span class="p">;</span></span>
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1024
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1003
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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="c"> </span>
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1025
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<td class="new_line diff-line-num old" data-linenumber="1004" 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="LC1025" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">stats</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1026
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<td class="new_line diff-line-num old" data-linenumber="1004" 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="LC1026" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendedFeatures</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1004" 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">
1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1005" 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">
1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="c"> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read_score</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1006" 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">
1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fragmentCounts</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1007" 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">
1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="c"> <span class="n" style="color: #333;">fragmentCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1027
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1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="c"> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1028
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1009
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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="c"> <span class="p">}</span></span>
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1029
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<td class="new_line diff-line-num old" data-linenumber="1010" 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="LC1029" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">frag_in_raw</span><span class="p">);</span></span>
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1030
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<td class="new_line diff-line-num old" data-linenumber="1010" 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="LC1030" 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;">stats</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="1031" 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">
1031
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<td class="new_line diff-line-num old" data-linenumber="1010" 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="LC1031" class="line" lang="c"> <span class="n" style="color: #333;">header</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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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1032
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<td class="new_line diff-line-num old" data-linenumber="1010" 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="LC1032" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1033" 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">
1033
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<td class="new_line diff-line-num old" data-linenumber="1010" 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="LC1033" class="line" lang="c"> <span class="n" style="color: #333;">sfread</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;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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;">frag_in_raw</span><span class="p">);</span></span>
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1034
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<td class="new_line diff-line-num old" data-linenumber="1010" 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="LC1034" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">header</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_in_raw</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1010" 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">
1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="c"> </span>
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1035
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<td class="new_line diff-line-num" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump frag info */</span></span>
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1036
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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;">alignFrag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Frag</span><span class="p">));</span></span>
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1037
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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;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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;">qseq</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1047" style="width: 35px; color: rgba(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="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1047,6 +1023,36 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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1047
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="c"> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrag</span><span class="p">;</span></span>
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1048
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1024
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="c"> </span>
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1049
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<td class="new_line diff-line-num" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">fragCount</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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<td class="new_line diff-line-num new" data-linenumber="1027" 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">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">stats</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1028" 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">
1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendedFeatures</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1029" 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">
1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="c"> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</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="p">}</span></span>
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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;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">frag_in_raw</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;">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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="c"> <span class="n" style="color: #333;">header</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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="c"> <span class="n" style="color: #333;">sfread</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;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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;">frag_in_raw</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;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">header</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_in_raw</span><span class="p">);</span></span>
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1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump frag info */</span></span>
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1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Frag</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1039" 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">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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;">qseq</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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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</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;">bestHits</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1041" 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">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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="p">(</span><span class="n" style="color: #333;">sparse</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">read_score</span><span class="p">;</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</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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<td class="new_line diff-line-num new" data-linenumber="1043" 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">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</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="new_line diff-line-num new" data-linenumber="1044" 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">
1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</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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<td class="new_line diff-line-num new" data-linenumber="1045" 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">
1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1046" 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">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</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;">ustrdup</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;">seq</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>
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<td class="new_line diff-line-num new" data-linenumber="1047" 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">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ustrdup</span><span class="p">(</span><span class="n" style="color: #333;">header</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;">header</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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<td class="new_line diff-line-num new" data-linenumber="1048" 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">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1049" 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">
1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="c"> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrag</span><span class="p">;</span></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="c"> </span>
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<td class="new_line diff-line-num new" data-linenumber="1051" 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">
1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">fragCount</span><span class="p">;</span></span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1053" 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">
1053
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<pre style="margin: 0;">+<span id="LC1053" 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;">stats</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1054" 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">
1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">frag_in_raw</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1055" 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">
1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="c"> <span class="n" style="color: #333;">sfseek</span><span class="p">(</span><span class="n" style="color: #333;">frag_in_raw</span><span class="p">,</span> <span class="n" style="color: #333;">stats</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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>
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1050
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1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="c"> <span class="p">}</span></span>
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1051
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1057
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="c"> </span>
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1052
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1058
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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fragCount</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">maxFrag</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">@@ -2029,7 +2035,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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2029
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2035
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<pre style="margin: 0;"> <span id="LC2035" class="line" lang="c"> <span class="p">}</span></span>
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2030
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2036
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<pre style="margin: 0;"> <span id="LC2036" class="line" lang="c"> </span>
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2031
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2037
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<pre style="margin: 0;"> <span id="LC2037" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tot</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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2032
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<pre style="margin: 0;">-<span id="LC2032" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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2038
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<pre style="margin: 0;">+<span id="LC2038" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplate</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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2033
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2039
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<pre style="margin: 0;"> <span id="LC2039" class="line" lang="c"> <span class="n" style="color: #333;">best_read_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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2034
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2040
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<pre style="margin: 0;"> <span id="LC2040" class="line" lang="c"> <span class="n" style="color: #333;">bestNum</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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2035
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2041
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<pre style="margin: 0;"> <span id="LC2041" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2094" style="width: 35px; color: rgba(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="2100" style="width: 35px; color: rgba(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">@@ -2094,38 +2100,14 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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2094
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2100
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<pre style="margin: 0;"> <span id="LC2100" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">;</span></span>
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2095
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2101
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<pre style="margin: 0;"> <span id="LC2101" class="line" lang="c"> <span class="n" style="color: #333;">strrc</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;">seq</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>
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2096
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2102
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<pre style="margin: 0;"> <span id="LC2102" class="line" lang="c"> <span class="p">}</span></span>
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2097
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<pre style="margin: 0;">-<span id="LC2097" class="line" lang="c"> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read_score</span><span class="p">;</span></span>
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2098
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<pre style="margin: 0;">-<span id="LC2098" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fragmentCounts</span><span class="p">)</span> <span class="p">{</span></span>
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2099
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<pre style="margin: 0;">-<span id="LC2099" class="line" lang="c"> <span class="n" style="color: #333;">fragmentCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2100
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<pre style="margin: 0;">-<span id="LC2100" class="line" lang="c"> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2101
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<pre style="margin: 0;">-<span id="LC2101" class="line" lang="c"> <span class="p">}</span></span>
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2102
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<pre style="margin: 0;">-<span id="LC2102" class="line" lang="c"> </span>
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2103
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<pre style="margin: 0;">-<span id="LC2103" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump frag info */</span></span>
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2104
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<pre style="margin: 0;">-<span id="LC2104" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Frag</span><span class="p">));</span></span>
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2105
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<pre style="margin: 0;">-<span id="LC2105" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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;">qseq</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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2106
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<pre style="margin: 0;">-<span id="LC2106" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</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;">bestHits</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2107" 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">
2107
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2107" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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="p">(</span><span class="n" style="color: #333;">sparse</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">read_score</span><span class="p">;</span></span>
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2108
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2108" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</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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2109
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2109" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</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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2110
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2110" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</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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<td class="old_line diff-line-num old" data-linenumber="2111" 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">
2111
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2111" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2112" 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">
2112
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2112" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</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;">ustrdup</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;">seq</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>
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<td class="old_line diff-line-num old" data-linenumber="2113" 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">
2113
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2113" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ustrdup</span><span class="p">(</span><span class="n" style="color: #333;">header</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;">header</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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<td class="old_line diff-line-num old" data-linenumber="2114" 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">
2114
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2114" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2115" 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">
2115
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2115" class="line" lang="c"> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrag</span><span class="p">;</span></span>
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2116
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2116" class="line" lang="c"> </span>
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2117
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<td class="new_line diff-line-num old" data-linenumber="2103" 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="LC2117" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">fragCount</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2118
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<td class="new_line diff-line-num" data-linenumber="2103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2103
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<pre style="margin: 0;"> <span id="LC2103" class="line" lang="c"> </span>
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<td class="old_line diff-line-num old" data-linenumber="2119" 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">
2119
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<td class="new_line diff-line-num old" data-linenumber="2104" 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="LC2119" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">stats</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="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="2120" 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">
2120
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<td class="new_line diff-line-num old" data-linenumber="2104" 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="LC2120" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendedFeatures</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2121" 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="2104" 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">
2104
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<pre style="margin: 0;">+<span id="LC2104" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2105" 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">
2105
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<pre style="margin: 0;">+<span id="LC2105" class="line" lang="c"> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read_score</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2106" 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">
2106
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<pre style="margin: 0;">+<span id="LC2106" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fragmentCounts</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2107" 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">
2107
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<pre style="margin: 0;">+<span id="LC2107" class="line" lang="c"> <span class="n" style="color: #333;">fragmentCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2121
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2108
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<pre style="margin: 0;"> <span id="LC2108" class="line" lang="c"> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2122
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2109
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<pre style="margin: 0;"> <span id="LC2109" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC2123" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">frag_in_raw</span><span class="p">);</span></span>
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2124
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<td class="new_line diff-line-num old" data-linenumber="2110" 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="LC2124" 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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2125
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<pre style="margin: 0;">-<span id="LC2125" class="line" lang="c"> <span class="n" style="color: #333;">header</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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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2126
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<pre style="margin: 0;">-<span id="LC2126" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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2127
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<pre style="margin: 0;">-<span id="LC2127" class="line" lang="c"> <span class="n" style="color: #333;">sfread</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;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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;">frag_in_raw</span><span class="p">);</span></span>
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2128
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<pre style="margin: 0;">-<span id="LC2128" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">header</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_in_raw</span><span class="p">);</span></span>
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2110
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<pre style="margin: 0;">+<span id="LC2110" class="line" lang="c"> </span>
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2129
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2111
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<pre style="margin: 0;"> <span id="LC2111" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump frag info */</span></span>
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2130
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2112
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<pre style="margin: 0;"> <span id="LC2112" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Frag</span><span class="p">));</span></span>
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2131
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2113
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<pre style="margin: 0;"> <span id="LC2113" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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;">qseq</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2141" style="width: 35px; color: rgba(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">@@ -2141,6 +2123,36 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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2141
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<pre style="margin: 0;"> <span id="LC2123" class="line" lang="c"> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrag</span><span class="p">;</span></span>
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2142
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2124
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<pre style="margin: 0;"> <span id="LC2124" class="line" lang="c"> </span>
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2143
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<pre style="margin: 0;"> <span id="LC2125" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">fragCount</span><span class="p">;</span></span>
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2126
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<pre style="margin: 0;">+<span id="LC2126" class="line" lang="c"> </span>
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2127
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<pre style="margin: 0;">+<span id="LC2127" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">stats</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="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="LC2128" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendedFeatures</span><span class="p">)</span> <span class="p">{</span></span>
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2129
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<pre style="margin: 0;">+<span id="LC2129" class="line" lang="c"> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2130" class="line" lang="c"> <span class="p">}</span></span>
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2131
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<pre style="margin: 0;">+<span id="LC2131" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">frag_in_raw</span><span class="p">);</span></span>
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2132
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<pre style="margin: 0;">+<span id="LC2132" 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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2133
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<pre style="margin: 0;">+<span id="LC2133" class="line" lang="c"> <span class="n" style="color: #333;">header</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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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2134
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<pre style="margin: 0;">+<span id="LC2134" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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2135
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<pre style="margin: 0;">+<span id="LC2135" class="line" lang="c"> <span class="n" style="color: #333;">sfread</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;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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;">frag_in_raw</span><span class="p">);</span></span>
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2136
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<pre style="margin: 0;">+<span id="LC2136" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">header</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_in_raw</span><span class="p">);</span></span>
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2137
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<pre style="margin: 0;">+<span id="LC2137" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump frag info */</span></span>
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2138
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<pre style="margin: 0;">+<span id="LC2138" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Frag</span><span class="p">));</span></span>
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2139
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<pre style="margin: 0;">+<span id="LC2139" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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;">qseq</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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2140
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<pre style="margin: 0;">+<span id="LC2140" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</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;">bestHits</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2141" 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">
2141
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<pre style="margin: 0;">+<span id="LC2141" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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="p">(</span><span class="n" style="color: #333;">sparse</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">read_score</span><span class="p">;</span></span>
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2142
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<pre style="margin: 0;">+<span id="LC2142" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</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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2143
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<pre style="margin: 0;">+<span id="LC2143" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</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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2144
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<pre style="margin: 0;">+<span id="LC2144" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</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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2145
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<pre style="margin: 0;">+<span id="LC2145" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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2146
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<pre style="margin: 0;">+<span id="LC2146" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</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;">ustrdup</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;">seq</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>
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2147
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<pre style="margin: 0;">+<span id="LC2147" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ustrdup</span><span class="p">(</span><span class="n" style="color: #333;">header</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;">header</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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2148
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<pre style="margin: 0;">+<span id="LC2148" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">];</span></span>
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2149
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<pre style="margin: 0;">+<span id="LC2149" class="line" lang="c"> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrag</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2150" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC2151" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">fragCount</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2152" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2153" 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;">stats</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2154
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<pre style="margin: 0;">+<span id="LC2154" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">frag_in_raw</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2155" class="line" lang="c"> <span class="n" style="color: #333;">sfseek</span><span class="p">(</span><span class="n" style="color: #333;">frag_in_raw</span><span class="p">,</span> <span class="n" style="color: #333;">stats</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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2156" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2157" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC2158" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fragCount</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">maxFrag</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#7d21f6d2a4876afc9692035ab8b768c7552662bb"><strong>seqparse.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">@@ -532,32 +532,34 @@ int FileBuffgetFqSeq(FileBuff *src, Qseqs *qseq, Qseqs *qual, char *trans) {</td>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getPhredFileBuff</span><span class="p">(</span><span class="n" style="color: #333;">FileBuff</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seek</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seek</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">avail</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">scale</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC536" 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;">buff</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="c"> <span class="n" style="color: #333;">avail</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bytes</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="c"> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">33</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="c"> <span class="n" style="color: #333;">buff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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="LC540" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">buff</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 right">0</span></span><span class="p">)</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="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">avail</span></span><span class="p">)</span> <span class="p">{</span></span>
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541
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="c"> <span class="n" style="color: #333;">seek</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</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="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">seek</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">buff</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 right">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">seek</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">--</span></span><span class="n" style="color: #333;"><span class="idiff right">avail</span></span><span class="p">)</span> <span class="p">{</span></span>
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543
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545
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<pre style="margin: 0;"> <span id="LC545" 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;">buff</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="p">{</span></span>
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544
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546
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">seek</span><span class="p">;</span></span>
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545
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="c"> <span class="p">}</span></span>
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548
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="c"> <span class="p">}</span></span>
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549
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="c"> <span class="n" style="color: #333;">seek</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">seek</span><span class="p">)</span> <span class="p">{</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="c"> <span class="n" style="color: #333;">seek</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">avail</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">1</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 right">0</span></span><span class="p">;</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">seek</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">--</span></span><span class="n" style="color: #333;"><span class="idiff right">avail</span></span><span class="p">)</span> <span class="p">{</span></span>
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550
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552
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<pre style="margin: 0;"> <span id="LC552" 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;">buff</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="p">{</span></span>
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551
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553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="c"> <span class="n" style="color: #333;">seek</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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552
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554
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<pre style="margin: 0;"> <span id="LC554" 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;">buff</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">33</span><span class="p">)</span> <span class="p">{</span></span>
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553
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555
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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554
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556
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<pre style="margin: 0;"> <span id="LC556" 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="mi" style="color: #099;">53</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buff</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buff</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">59</span><span class="p">)</span> <span class="p">{</span></span>
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">33</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC556" 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;">buff</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">84</span></span><span class="p">)</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;"><span class="idiff left right">return</span></span> <span class="mi" style="color: #099;">64</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC558" 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="mi" style="color: #099;"><span class="idiff left">94</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buff</span><span class="p">)</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;"><span class="idiff left">scale</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="mi" style="color: #099;">64</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>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</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="LC564" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">scale</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#f80652dda49a7117428c0f92935664fc8cd4e2d1"><strong>spltdb.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">@@ -1226,7 +1226,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<pre style="margin: 0;"> <span id="LC1226" class="line" lang="c"> <span class="p">}</span></span>
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1227
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<pre style="margin: 0;"> <span id="LC1227" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC1228" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tot</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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1229
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<pre style="margin: 0;">-<span id="LC1229" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left">-</span></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="LC1229" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplate</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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1230
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<pre style="margin: 0;"> <span id="LC1230" class="line" lang="c"> <span class="n" style="color: #333;">best_read_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="LC1231" class="line" lang="c"> <span class="n" style="color: #333;">bestNum</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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1232
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<pre style="margin: 0;"> <span id="LC1232" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1291" style="width: 35px; color: rgba(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">@@ -1291,38 +1291,14 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="c"> <span class="n" style="color: #333;">strrc</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;">seq</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>
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1293
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<pre style="margin: 0;"> <span id="LC1293" class="line" lang="c"> <span class="p">}</span></span>
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1294
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<pre style="margin: 0;">-<span id="LC1294" class="line" lang="c"> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read_score</span><span class="p">;</span></span>
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1295
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<pre style="margin: 0;">-<span id="LC1295" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fragmentCounts</span><span class="p">)</span> <span class="p">{</span></span>
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1296
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<pre style="margin: 0;">-<span id="LC1296" class="line" lang="c"> <span class="n" style="color: #333;">fragmentCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1297" 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">
1297
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<pre style="margin: 0;">-<span id="LC1297" class="line" lang="c"> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1298
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<pre style="margin: 0;">-<span id="LC1298" class="line" lang="c"> <span class="p">}</span></span>
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1299
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1299" class="line" lang="c"> </span>
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1300
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1300" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump frag info */</span></span>
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1301
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1301" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Frag</span><span class="p">));</span></span>
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1302
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1302" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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;">qseq</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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<td class="old_line diff-line-num old" data-linenumber="1303" 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">
1303
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1303" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</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;">bestHits</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1304" 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">
1304
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1304" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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="p">(</span><span class="n" style="color: #333;">sparse</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">read_score</span><span class="p">;</span></span>
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1305
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1305" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</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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<td class="old_line diff-line-num old" data-linenumber="1306" 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">
1306
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1306" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</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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1307
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1307" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</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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<td class="old_line diff-line-num old" data-linenumber="1308" 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">
1308
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1308" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<td class="old_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">
1309
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1309" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</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;">ustrdup</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;">seq</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>
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<td class="old_line diff-line-num old" data-linenumber="1310" 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">
1310
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1310" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ustrdup</span><span class="p">(</span><span class="n" style="color: #333;">header</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;">header</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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<td class="old_line diff-line-num old" data-linenumber="1311" 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">
1311
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1311" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">];</span></span>
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1312
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<td class="new_line diff-line-num old" data-linenumber="1294" 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="LC1312" class="line" lang="c"> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrag</span><span class="p">;</span></span>
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1313
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1294
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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="c"> </span>
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1314
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<td class="new_line diff-line-num old" data-linenumber="1295" 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="LC1314" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left">++</span></span><span class="n" style="color: #333;"><span class="idiff">fragCount</span></span><span class="p"><span class="idiff right">;</span></span></span>
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1315
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<td class="new_line diff-line-num old" data-linenumber="1295" 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="LC1315" class="line" lang="c"> </span>
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<td class="old_line diff-line-num old" data-linenumber="1316" 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">
1316
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<td class="new_line diff-line-num old" data-linenumber="1295" 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="LC1316" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">stats</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</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="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1317" 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">
1317
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<td class="new_line diff-line-num old" data-linenumber="1295" 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="LC1317" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">extendedFeatures</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="1318" 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="1295" 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">
1295
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">bestTemplate</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="1318" 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="1296" 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">
1296
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">w_scores</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">bestTemplate</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">read_score</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="1297" 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">
1297
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="c"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff right">fragmentCounts</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1318" 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="1298" 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">
1298
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">fragmentCounts</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">bestTemplate</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="old_line diff-line-num" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1318
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<td class="new_line diff-line-num" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="c"> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1319
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<td class="new_line diff-line-num" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1300
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1320" 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">
1320
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<td class="new_line diff-line-num old" data-linenumber="1301" 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="LC1320" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">frag_in_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1321" 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">
1321
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<td class="new_line diff-line-num old" data-linenumber="1301" 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="LC1321" 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;">stats</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="1322" 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">
1322
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<td class="new_line diff-line-num old" data-linenumber="1301" 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="LC1322" class="line" lang="c"> <span class="n" style="color: #333;">header</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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1323" 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">
1323
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<td class="new_line diff-line-num old" data-linenumber="1301" 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="LC1323" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1324" 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">
1324
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<td class="new_line diff-line-num old" data-linenumber="1301" 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="LC1324" class="line" lang="c"> <span class="n" style="color: #333;">sfread</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;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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;">frag_in_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1325" 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">
1325
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<td class="new_line diff-line-num old" data-linenumber="1301" 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="LC1325" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">header</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_in_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1326" 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="1301" 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">
1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="c"> </span>
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1326
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<td class="new_line diff-line-num" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump frag info */</span></span>
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<td class="old_line diff-line-num" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1327
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<td class="new_line diff-line-num" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Frag</span><span class="p">));</span></span>
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1328
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1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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;">qseq</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1338,8 +1314,39 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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1338
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1314
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<pre style="margin: 0;"> <span id="LC1314" class="line" lang="c"> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrag</span><span class="p">;</span></span>
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1339
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1315
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<pre style="margin: 0;"> <span id="LC1315" class="line" lang="c"> </span>
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1340
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1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">fragCount</span><span class="p">;</span></span>
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1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="c"> </span>
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1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">stats</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1319" 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">
1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendedFeatures</span><span class="p">)</span> <span class="p">{</span></span>
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1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="c"> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="c"> <span class="p">}</span></span>
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1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">frag_in_raw</span><span class="p">);</span></span>
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1323
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<pre style="margin: 0;">+<span id="LC1323" 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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1324
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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="c"> <span class="n" style="color: #333;">header</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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="c"> <span class="n" style="color: #333;">sfread</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;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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;">frag_in_raw</span><span class="p">);</span></span>
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1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">header</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_in_raw</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1328" 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">
1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* dump frag info */</span></span>
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1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Frag</span><span class="p">));</span></span>
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1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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;">qseq</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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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</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;">bestHits</span><span class="p">;</span></span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</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="p">(</span><span class="n" style="color: #333;">sparse</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">read_score</span><span class="p">;</span></span>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</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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<td class="new_line diff-line-num new" data-linenumber="1334" 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">
1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</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="new_line diff-line-num new" data-linenumber="1335" 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">
1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</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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<td class="new_line diff-line-num new" data-linenumber="1336" 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">
1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</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;">ustrdup</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;">seq</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>
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<td class="new_line diff-line-num new" data-linenumber="1338" 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">
1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ustrdup</span><span class="p">(</span><span class="n" style="color: #333;">header</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;">header</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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<td class="new_line diff-line-num new" data-linenumber="1339" 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">
1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="c"> <span class="n" style="color: #333;">alignFrag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">];</span></span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="c"> <span class="n" style="color: #333;">alignFrags</span><span class="p">[</span><span class="n" style="color: #333;">bestTemplate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignFrag</span><span class="p">;</span></span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="c"> </span>
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1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">fragCount</span><span class="p">;</span></span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1344" 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">
1344
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<pre style="margin: 0;">+<span id="LC1344" 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;">stats</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1345" 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">
1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="c"> <span class="n" style="color: #333;">sfread</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">frag_in_raw</span><span class="p">);</span></span>
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1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="c"> <span class="n" style="color: #333;">sfseek</span><span class="p">(</span><span class="n" style="color: #333;">frag_in_raw</span><span class="p">,</span> <span class="n" style="color: #333;">stats</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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>
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1341
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1347
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="c"> <span class="p">}</span></span>
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1342
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1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="c"> </span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="c"> </span>
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1343
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1350
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<pre style="margin: 0;"> <span id="LC1350" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fragCount</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">maxFrag</span><span class="p">)</span> <span class="p">{</span></span>
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1344
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1351
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="c"> <span class="n" style="color: #333;">template_fragments</span><span class="p">[</span><span class="n" style="color: #333;">fileCount</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">printFrags</span><span class="p">(</span><span class="n" style="color: #333;">alignFrags</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">fileCount</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">@@ -238,7 +238,7 @@ double eQual(unsigned char *qual, int len, int phredScale, int minQ) {</td>
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<pre style="margin: 0;"> <span id="LC238" 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="LC239" 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="LC240" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">double</span></span> <span class="nf" style="color: #900; font-weight: 600;">eQual</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;">qual</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;">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;">minQ</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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="nf" style="color: #900; font-weight: 600;">eQual</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;">qual</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;">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;">minQ</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="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;">/*</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;"> static const double prob[128] = {</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">@@ -277,5 +277,5 @@ double eQual(unsigned char *qual, const int len, const int minQ, const double *p</td>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* return average */</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">log10</span><span class="p">(</span><span class="n" style="color: #333;">sum</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="LC280" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">ceil</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">log10</span><span class="p">(</span><span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">len</span><span class="p">)<span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#54798841eb38daaad8bb0e117d6d873232389f69"><strong>stdstat.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">@@ -29,4 +29,4 @@ double p_chisqr(long double q);</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;">double</span> <span class="nf" style="color: #900; font-weight: 600;">power</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">binP</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</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;">double</span> <span class="n" style="color: #333;">p</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;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">minimum</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;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">double</span></span> <span class="nf" style="color: #900; font-weight: 600;">eQual</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;">qual</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;">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;">minQ</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></pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="nf" style="color: #900; font-weight: 600;">eQual</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;">qual</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;">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;">minQ</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></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#1c6375d34d9e418d1139bd146337fb256ac24a2a"><strong>tmp.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">@@ -27,7 +27,7 @@</td>
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<pre style="margin: 0;"> <span id="LC27" 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="nf" style="color: #900; font-weight: 600;">tmpF</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">location</span><span class="p">)</span> <span class="p">{</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="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmpNum</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="LC30" 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;">tmpname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dirname</span> <span class="o" style="font-weight: 600;">=</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;">filename</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="LC30" 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;">tmpname</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">0</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dirname</span> <span class="o" style="font-weight: 600;">=</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;">filename</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="LC31" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Lock</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="LC32" class="line" lang="c"> <span class="k" style="font-weight: 600;">volatile</span> <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;">lock</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Lock</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fd</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">@@ -66,11 +66,22 @@ FILE * tmpF(const char *location) {</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">tmpname</span><span class="p">,</span> <span class="s" style="color: #d14;">"XXXXXX"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC67" 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;">filename</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;">/* open tmpfile on previous location */</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tmpname</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">tmpNum</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">fd</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;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tmpname</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">tmpNum</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb+"</span><span class="p">)))</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;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">filename</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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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpname</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="LC74" 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;">tmpNum</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* set default according to TMPDIR */</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">tmpname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getenv</span><span class="p">(</span><span class="s" style="color: #d14;">"TMPDIR"</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">dirname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tmpname</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">13</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">tmpname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dirname</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">dirname</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s/.kma-"</span><span class="p">,</span> <span class="n" style="color: #333;">tmpname</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;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">tmpname</span><span class="p">,</span> <span class="s" style="color: #d14;">"XXXXXX"</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>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"> <span class="n" style="color: #333;">tmpNum</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="LC82" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tmpF</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC85" 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="LC86" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* open a "normal" tmp file */</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpfile</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">@@ -79,13 +90,3 @@ FILE * tmpF(const char *location) {</td>
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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;">return</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#f568890dac40d04b36ce5786c44ac5704d31fe78"><strong>updateindex.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">@@ -114,7 +114,7 @@ int updateDBs_sparse(HashMap *templates, CompDNA *qseq, unsigned template, int M</td>
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<pre style="margin: 0;"> <span id="LC114" 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;">N</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="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prefix_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="LC117" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prefix_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff right">prefix</span></span><span class="p">)</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;">comp_rc</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/e82ae7fe11bf6575b1606f2fb1445ac73c6e0f5f#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 "1.3.2<span class="idiff left right">3</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 "1.3.2<span class="idiff left right">8</span>"</span></span></pre>
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