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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/ff1b86fc8b79edacb3b1bc4eb9449a580b87c749">ff1b86fc</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-02-06T12:48:19+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/339b078952ca08927f0b733f18a91a69676c6ff7">339b0789</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-02-06T12:48:20+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.10</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/b59aaaa120018be036131d6dddc836948340439e">b59aaaa1</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-02-06T12:48:22+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.3.10'
Update to upstream version '1.3.10'
with Debian dir 4a703fda89239e0f8f5540d833d19876ef4f4fcc</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/0ff4ca082261352c3a65cc5c048700768a9f6bec">0ff4ca08</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-02-06T12:50:58+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix faulty VCS URL
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/3f30a8a2d9ec1aa92b0571c83151dc64afb8154c">3f30a8a2</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-02-06T12:51:58+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>19 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1ff221cada819d34daa6f89593fc3d48f1acc3ce">
KMAspecification.pdf
</a>
</li>
<li class="file-stats">
<a href="#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
align.c
</a>
</li>
<li class="file-stats">
<a href="#302e1fff50e6c455134afebd2f2fa2f0c5b717d8">
alnfrags.c
</a>
</li>
<li class="file-stats">
<a href="#7de51ef51edfe95b4295321baa1218f84d7960c9">
alnfrags.h
</a>
</li>
<li class="file-stats">
<a href="#99bf70d606be11e0793b7e3ba6c29182326341d6">
assembly.c
</a>
</li>
<li class="file-stats">
<a href="#51c40fb7131cdb8caf085506f3b96d589be532ff">
assembly.h
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#5bb411548ec4b39482e6de83d3ad98f29b1162b1">
kma.c
</a>
</li>
<li class="file-stats">
<a href="#088a2f1aaa170cd721dbae6f4b2bcb8239c7119a">
mt1.c
</a>
</li>
<li class="file-stats">
<a href="#1046a66b72dbb642e4d57ce820566e6c09c525d9">
mt1.h
</a>
</li>
<li class="file-stats">
<a href="#97e3379ce2e33418ea5b83d3faaf35326b973d41">
nw.c
</a>
</li>
<li class="file-stats">
<a href="#61a960d3b9862f2e47015c82850b2b590c708d06">
nw.h
</a>
</li>
<li class="file-stats">
<a href="#ca9efd475143efe0a1b0464c67f49900d98ca75a">
runkma.c
</a>
</li>
<li class="file-stats">
<a href="#96f176d59b0bd765be8443801e2c6244ae632120">
runkma.h
</a>
</li>
<li class="file-stats">
<a href="#3ff76aca17d9815adbbfee02596e6c4d46aa1384">
sam.c
</a>
</li>
<li class="file-stats">
<a href="#f80652dda49a7117428c0f92935664fc8cd4e2d1">
spltdb.c
</a>
</li>
<li class="file-stats">
<a href="#e55b6b603fd8c696cd5ece7be98d78898a9ee58f">
spltdb.h
</a>
</li>
<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="1ff221cada819d34daa6f89593fc3d48f1acc3ce">
<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#1ff221cada819d34daa6f89593fc3d48f1acc3ce"><strong>KMAspecification.pdf</strong></a>
<hr>
No preview for this file type
<br>
</li>
<li id="ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40"><strong>align.c</strong></a>
<hr>
<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="200" 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="200" 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">@@ -200,6 +200,7 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="200" 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">
200
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<td class="diff-line-num new_line" data-linenumber="200" 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">
200
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="201" 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">
201
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<td class="diff-line-num new_line" data-linenumber="201" 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">
201
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="202" 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">
202
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<td class="diff-line-num new_line" data-linenumber="202" 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">
202
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="203" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
203
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<td class="diff-line-num new_line" data-linenumber="204" 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">
204
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="204" 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">
204
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<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
205
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
205
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<td class="diff-line-num new_line" data-linenumber="206" 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">
206
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="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="p">;</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="214" 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="215" 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">@@ -214,6 +215,7 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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<td class="diff-line-num old_line" data-linenumber="214" 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">
214
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<td class="diff-line-num new_line" data-linenumber="215" 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="LC215" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mapQ</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="215" 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">
215
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<td class="diff-line-num new_line" data-linenumber="216" 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="LC216" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="216" 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">
216
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<td class="diff-line-num new_line" data-linenumber="217" 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="LC217" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="217" 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">
217
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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC219" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="218" 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">
218
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<td class="diff-line-num new_line" data-linenumber="220" 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">
220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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219
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="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="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="227" 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">@@ -225,6 +227,7 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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225
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* initialize */</span></span>
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226
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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227
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<td class="diff-line-num new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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228
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<td class="diff-line-num new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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229
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="c"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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230
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="278" 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="281" 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">@@ -278,6 +281,7 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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278
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<td class="diff-line-num new_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
279
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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280
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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281
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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282
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286
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<pre style="margin: 0;"> <span id="LC286" 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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283
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_s</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="294" 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="298" 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">@@ -294,6 +298,7 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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294
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<td class="diff-line-num new_line" data-linenumber="298" 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">
298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="sc" style="color: #d14;">'|'</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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295
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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296
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="301" 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">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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297
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<td class="diff-line-num new_line" data-linenumber="302" 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">
302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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298
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="299" 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">
299
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c"> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="334" 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="339" 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">@@ -334,6 +339,7 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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334
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<td class="diff-line-num new_line" data-linenumber="339" 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">
339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap is too big to give a positive score */</span></span>
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<td class="diff-line-num old_line" data-linenumber="335" 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">
335
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<td class="diff-line-num new_line" data-linenumber="340" 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">
340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="336" 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">
336
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<td class="diff-line-num new_line" data-linenumber="341" 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">
341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="342" 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">
342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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337
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<td class="diff-line-num new_line" data-linenumber="343" 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">
343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="338" 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">
338
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="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="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="339" 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">
339
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="354" 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="360" 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">@@ -354,6 +360,7 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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<td class="diff-line-num old_line" data-linenumber="354" 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">
354
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<td class="diff-line-num new_line" data-linenumber="360" 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">
360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="355" 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">
355
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<td class="diff-line-num new_line" data-linenumber="361" 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">
361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="356" 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">
356
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<td class="diff-line-num new_line" data-linenumber="362" 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">
362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="363" 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">
363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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357
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<td class="diff-line-num new_line" data-linenumber="364" 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">
364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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358
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="c"> <span class="p">}</span></span>
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359
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="417" 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">@@ -410,6 +417,7 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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410
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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411
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<td class="diff-line-num new_line" data-linenumber="418" 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">
418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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412
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="420" 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">
420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="413" 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">
413
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<td class="diff-line-num new_line" data-linenumber="421" 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">
421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="414" 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">
414
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<td class="diff-line-num new_line" data-linenumber="422" 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">
422
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<pre style="margin: 0;"> <span id="LC422" 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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415
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c"> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="560" 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="568" 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">@@ -560,6 +568,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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560
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<td class="diff-line-num new_line" data-linenumber="568" 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">
568
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<pre style="margin: 0;"> <span id="LC568" 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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561
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<td class="diff-line-num new_line" data-linenumber="569" 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">
569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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562
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<td class="diff-line-num new_line" data-linenumber="570" 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">
570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="563" 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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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="563" 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">
563
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<td class="diff-line-num new_line" data-linenumber="572" 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">
572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="564" 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">
564
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<td class="diff-line-num new_line" data-linenumber="573" 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">
573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="565" 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">
565
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<td class="diff-line-num new_line" data-linenumber="574" 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">
574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="574" 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="583" 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">@@ -574,6 +583,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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574
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<td class="diff-line-num new_line" data-linenumber="583" 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">
583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mapQ</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="575" 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">
575
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<td class="diff-line-num new_line" data-linenumber="584" 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">
584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="576" 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">
576
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<td class="diff-line-num new_line" data-linenumber="585" 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">
585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="577" 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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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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577
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="578" 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">
578
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="579" 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">
579
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="583" 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="593" 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">@@ -583,6 +593,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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583
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<td class="diff-line-num new_line" data-linenumber="593" 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">
593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* initialize */</span></span>
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584
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<td class="diff-line-num new_line" data-linenumber="594" 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">
594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="585" 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">
585
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<td class="diff-line-num new_line" data-linenumber="595" 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">
595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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586
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<td class="diff-line-num new_line" data-linenumber="597" 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">
597
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="587" 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">
587
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="c"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="588" 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">
588
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="615" 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="626" 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">@@ -615,6 +626,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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615
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626
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="616" 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">
616
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627
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="617" 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">
617
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="629" 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">
629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="618" 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">
618
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630
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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619
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631
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="c"> <span class="p">}</span></span>
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620
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="626" 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="638" 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">@@ -626,6 +638,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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626
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="c"> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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627
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639
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_s</span><span class="p">;</span></span>
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628
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640
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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629
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642
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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630
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643
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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631
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644
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="c"> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="665" 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="678" 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">@@ -665,6 +678,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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665
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678
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap is too big to give a positive score */</span></span>
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<td class="diff-line-num old_line" data-linenumber="666" 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">
666
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<td class="diff-line-num new_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
679
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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667
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680
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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668
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682
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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669
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683
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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670
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684
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Stat</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="678" 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="692" 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">@@ -678,6 +692,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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678
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="c"> <span class="p">}</span></span>
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679
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693
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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680
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694
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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681
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696
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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682
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697
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="c"> <span class="p">}</span></span>
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683
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698
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -711,6 +726,7 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#302e1fff50e6c455134afebd2f2fa2f0c5b717d8"><strong>alnfrags.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">@@ -35,12 +35,12 @@</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "threader.h"</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "updatescores.h"</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alnFragsPE</span><span class="p">)(</span><span class="n" style="color: #333;">HashMapCCI</span><span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</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;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">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;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="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="p">,</span> <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="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnFragsUnionPE</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alnFragsPE</span><span class="p">)(</span><span class="n" style="color: #333;">HashMapCCI</span><span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">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;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="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="p">,</span> <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="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnFragsUnionPE</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsSE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rc_flag</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">best_read_score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsSE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rc_flag</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">best_read_score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_i</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">arc</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_start</span><span class="p">,</span> <span class="n" style="color: #333;">q_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qBoundPtr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_start</span><span class="p">,</span> <span class="n" style="color: #333;">q_end</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">t_len</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qBoundPtr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">AlnScore</span> <span class="n" style="color: #333;">alnStat</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC46" 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">@@ -118,14 +118,15 @@ int alnFragsSE(HashMapCCI **templates_index, int *matched_templates, int *templa</td>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">template</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">template</span><span class="p">)];</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">template</span><span class="p">)]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">q_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">q_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">template</span><span class="p">)];</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* penalty for non complete mapping */</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* full gene award */</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left">emplate_lengths</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">template</span></span><span class="p"><span class="idiff right">)]</span>))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left right">_len</span></span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">W1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//read_score += (((start != 0) + (end != template_lengths[abs(template)])) * W1);</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">@@ -174,10 +175,10 @@ int alnFragsSE(HashMapCCI **templates_index, int *matched_templates, int *templa</td>
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<pre style="margin: 0;"> <span id="LC175" 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="LC176" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsUnionPE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsUnionPE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_i</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits_r</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">arc</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits_r</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">t_len</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">arc</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="c"> <span class="n" style="color: #333;">AlnScore</span> <span class="n" style="color: #333;">alnStat</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC184" 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">@@ -256,10 +257,11 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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256
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get read score */</span></span>
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257
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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258
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</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 class="p">{</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">template</span><span class="p">)];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</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="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">)</span> <span class="p">{</span></span>
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260
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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261
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left">emplate_lengths</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">template</span></span><span class="p"><span class="idiff right">)]</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left right">_len</span></span><span class="p">)</span> <span class="p">{</span></span>
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263
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">W1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">aln_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">@@ -302,11 +304,11 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get read score */</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">t_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="n" style="color: #333;"><span class="idiff">qseq_r_comp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">seqlen</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">mrc</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">t_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="n" style="color: #333;"><span class="idiff">mrc</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">qseq_r_comp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">seqlen</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">alnStat</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">match</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left">emplate_lengths</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">template</span></span><span class="p"><span class="idiff right">)]</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left right">_len</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">W1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">aln_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">@@ -339,7 +341,7 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">t_i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">t_i</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;">best_end_pos</span><span class="p">[</span><span class="n" style="color: #333;">t_i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left">emplate_lengths</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">template</span></span><span class="p"><span class="idiff right">)]</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">t_i</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;">best_end_pos</span><span class="p">[</span><span class="n" style="color: #333;">t_i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left right">_len</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">W1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">compScore</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">read_score</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">@@ -501,10 +503,10 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsPenaltyPE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsPenaltyPE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="c"> </span>
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_i</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">PE</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits_r</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">arc</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits_r</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">t_len</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">arc</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="c"> <span class="n" style="color: #333;">AlnScore</span> <span class="n" style="color: #333;">alnStat</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC512" 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">@@ -584,11 +586,12 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get read score */</span></span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">template</span><span class="p">)];</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</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="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left">emplate_lengths</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">template</span></span><span class="p"><span class="idiff right">)]</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left right">_len</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">W1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">aln_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">@@ -629,11 +632,11 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get read score */</span></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">t_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="n" style="color: #333;"><span class="idiff">qseq_r_comp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">seqlen</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">mrc</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">t_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="n" style="color: #333;"><span class="idiff">mrc</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">qseq_r_comp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">seqlen</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">alnStat</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">match</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left">emplate_lengths</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">template</span></span><span class="p"><span class="idiff right">)]</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left right">_len</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">W1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">aln_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">@@ -825,9 +828,10 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsForcePE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsForcePE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">)</span> <span class="p">{</span></span>
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="c"> </span>
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_i</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">arc</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="p">;</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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832
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="c"> <span class="n" style="color: #333;">AlnScore</span> <span class="n" style="color: #333;">alnStat</span><span class="p">,</span> <span class="n" style="color: #333;">alnStat_r</span><span class="p">;</span></span>
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833
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<pre style="margin: 0;"> <span id="LC837" 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">@@ -902,7 +906,8 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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906
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<pre style="margin: 0;"> <span id="LC906" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">KMA_score</span><span class="p">(</span><span class="n" style="color: #333;">templates_index</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">],</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmatrices</span><span class="p">);</span></span>
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="c"> <span class="p">}</span></span>
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC905" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">)</span> <span class="p">{</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">template</span><span class="p">)];</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">)</span> <span class="p">{</span></span>
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911
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">arc</span><span class="p">)</span> <span class="p">{</span></span>
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912
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rc</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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908
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* rc */</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">@@ -936,7 +941,7 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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941
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<pre style="margin: 0;"> <span id="LC941" class="line" lang="c"> <span class="p">}</span></span>
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942
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="c"> </span>
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938
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alnStat_r</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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939
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<pre style="margin: 0;">-<span id="LC939" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left">emplate_lengths</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">template</span></span><span class="p"><span class="idiff right">)]</span>)</span> <span class="p">{</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">t<span class="idiff left right">_len</span></span><span class="p">)</span> <span class="p">{</span></span>
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940
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<pre style="margin: 0;"> <span id="LC945" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">W1</span><span class="p">);</span></span>
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941
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946
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<pre style="margin: 0;"> <span id="LC946" class="line" lang="c"> <span class="p">}</span></span>
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942
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947
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">aln_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">@@ -948,7 +953,7 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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948
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953
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<pre style="margin: 0;"> <span id="LC953" class="line" lang="c"> <span class="p">}</span></span>
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954
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="c"> </span>
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950
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955
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* save best match(es) */</span></span>
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951
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_score</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="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">scoreT</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_score</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="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">scoreT</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">t_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="n" style="color: #333;"><span class="idiff">qseq_r_comp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">seqlen</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">mrc</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">t_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="n" style="color: #333;"><span class="idiff">mrc</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">qseq_r_comp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">seqlen</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">alnStat</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">match</span></span><span class="p">)</span> <span class="p">{</span></span>
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952
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestScore</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// save as best match</span></span>
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953
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1016,7 +1021,7 @@ void * alnFrags_threaded(void * arg) {</td>
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">;</span></span>
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1017
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<td class="diff-line-num new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1022
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">;</span></span>
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1018
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1023
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<pre style="margin: 0;"> <span id="LC1023" 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;">qseq_fr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">;</span></span>
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1019
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<td class="diff-line-num new_line old" data-linenumber="1024" 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="LC1019" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1024" 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">
1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mrc</span></span><span class="p">;</span></span>
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1020
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<td class="diff-line-num new_line" 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="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1021" 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">
1021
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<td class="diff-line-num new_line" data-linenumber="1026" 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">
1026
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<pre style="margin: 0;"> <span id="LC1026" class="line" lang="c"> <span class="n" style="color: #333;">FileBuff</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_all</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1022
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<td class="diff-line-num new_line" data-linenumber="1027" 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">
1027
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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="c"> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1051,6 +1056,7 @@ void * alnFrags_threaded(void * arg) {</td>
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1051
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<td class="diff-line-num new_line" data-linenumber="1056" 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">
1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="c"> <span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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1052
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<td class="diff-line-num new_line" data-linenumber="1057" 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">
1057
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="c"> <span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1053" 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">
1053
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<td class="diff-line-num new_line" data-linenumber="1058" 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">
1058
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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="c"> <span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" data-linenumber="1059" 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">
1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="c"> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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1054
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<td class="diff-line-num new_line" data-linenumber="1060" 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">
1060
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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="c"> <span class="n" style="color: #333;">template_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_lengths</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1055" 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">
1055
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<td class="diff-line-num new_line" data-linenumber="1061" 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">
1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="c"> <span class="n" style="color: #333;">templates_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">templates_index</span><span class="p">;</span></span>
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1056
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<td class="diff-line-num new_line" data-linenumber="1062" 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">
1062
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<pre style="margin: 0;"> <span id="LC1062" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1103" 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="1109" 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">@@ -1103,9 +1109,9 @@ void * alnFrags_threaded(void * arg) {</td>
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<td class="diff-line-num old_line" data-linenumber="1103" 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">
1103
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1109
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="c"> </span>
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1104
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<td class="diff-line-num new_line" data-linenumber="1110" 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">
1110
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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</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 class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1105" 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">
1105
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<td class="diff-line-num new_line" data-linenumber="1111" 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">
1111
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_score</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="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// PE</span></span>
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1106
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<pre style="margin: 0;">-<span id="LC1106" class="line" lang="c"> <span class="n" style="color: #333;">unmapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnFragsPE</span><span class="p">(</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span><span class="p">,</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_rr_comp</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_r</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_fr</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_read_score</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 class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="n" style="color: #333;">excludeDB</span><span class="p">);</span></span>
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1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="c"> <span class="n" style="color: #333;">unmapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnFragsPE</span><span class="p">(</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span><span class="p">,</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">m<span class="idiff left">rc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m</span>inlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_rr_comp</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_r</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_fr</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_read_score</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 class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="n" style="color: #333;">excludeDB</span><span class="p">);</span></span>
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1107
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<td class="diff-line-num new_line" data-linenumber="1113" 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">
1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// SE</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1108" 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">
1108
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<td class="diff-line-num new_line old" data-linenumber="1114" 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="LC1108" class="line" lang="c"> <span class="n" style="color: #333;">unmapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnFragsSE</span><span class="p">(</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span><span class="p">,</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rc_flag</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</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_r</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="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="n" style="color: #333;">excludeDB</span><span class="p">);</span></span>
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1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="c"> <span class="n" style="color: #333;">unmapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnFragsSE</span><span class="p">(</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span><span class="p">,</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">m<span class="idiff left">rc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m</span>inlen</span><span class="p">,</span> <span class="n" style="color: #333;">rc_flag</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</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_r</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="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="n" style="color: #333;">excludeDB</span><span class="p">);</span></span>
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1109
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="c"> <span class="p">}</span></span>
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1110
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1116
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<pre style="margin: 0;"> <span id="LC1116" 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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1111
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1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="c"> <span class="n" style="color: #333;">unmapped</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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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#7de51ef51edfe95b4295321baa1218f84d7960c9"><strong>alnfrags.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">@@ -47,6 +47,7 @@ struct aln_thread {</td>
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47
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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48
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</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">@@ -60,9 +61,9 @@ struct aln_thread {</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define ALNTHREAD 1;</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="nf" style="color: #900; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alnFragsPE</span><span class="p">)(</span><span class="n" style="color: #333;">HashMapCCI</span><span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</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;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">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;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="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="p">,</span> <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="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsSE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rc_flag</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">best_read_score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsUnionPE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsPenaltyPE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">);</span></span>
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<td class="diff-line-num new_line old" data-linenumber="64" 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="LC67" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsForcePE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="nf" style="color: #900; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alnFragsPE</span><span class="p">)(</span><span class="n" style="color: #333;">HashMapCCI</span><span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">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;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="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="p">,</span> <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="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsSE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rc_flag</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">best_read_score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsUnionPE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsPenaltyPE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alnFragsForcePE</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templates_index</span><span class="p">,</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;">matched_templates</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr_comp</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr_comp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_fr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_rr</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</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;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">best_start_pos</span><span class="p">,</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;">best_end_pos</span><span class="p">,</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;">flag</span><span class="p">,</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;">flag_r</span><span class="p">,</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;">best_read_score</span><span class="p">,</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;">best_read_score_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">,</span> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">,</span> <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;">excludeOut</span><span class="p">,</span> <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;">excludeDB</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">alnFrags_threaded</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arg</span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#99bf70d606be11e0793b7e3ba6c29182326341d6"><strong>assembly.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">@@ -283,7 +283,7 @@ void * assemble_KMA_threaded(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="n" style="color: #333;">depthVar</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</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;">counts</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC285" 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="LC286" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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287
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">bestNuc</span><span class="p">;</span></span>
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288
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">files</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">xml_out</span><span class="p">;</span></span>
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c"> <span class="n" style="color: #333;">AlnScore</span> <span class="n" style="color: #333;">alnStat</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -314,6 +314,7 @@ void * assemble_KMA_threaded(void *arg) {</td>
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314
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c"> <span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"> <span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"> <span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="c"> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="c"> <span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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318
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c"> <span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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319
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="c"> <span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="433" 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="434" 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">@@ -433,9 +434,9 @@ void * assemble_KMA_threaded(void *arg) {</td>
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433
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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434
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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435
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get normed score */</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get normed score <span class="idiff left right">check read coverage </span>*/</span></span>
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437
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">t_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="n" style="color: #333;"><span class="idiff">qseq</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">)</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">mrc</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">t_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="n" style="color: #333;"><span class="idiff">mrc</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">qseq</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">)</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">alnStat</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">match</span></span><span class="p">)</span> <span class="p">{</span></span>
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440
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">aln_len</span><span class="p">;</span></span>
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440
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441
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<pre style="margin: 0;"> <span id="LC441" 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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442
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="c"> <span class="n" style="color: #333;">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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -781,7 +782,7 @@ void * assemble_KMA_dense_threaded(void *arg) {</td>
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782
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="n" style="color: #333;">depthVar</span><span class="p">;</span></span>
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782
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783
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</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;">counts</span><span class="p">;</span></span>
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783
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784
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<pre style="margin: 0;"> <span id="LC784" 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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784
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<pre style="margin: 0;">-<span id="LC784" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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785
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">bestNuc</span><span class="p">;</span></span>
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786
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">files</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">xml_out</span><span class="p">;</span></span>
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787
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="c"> <span class="n" style="color: #333;">AlnScore</span> <span class="n" style="color: #333;">alnStat</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="812" 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">@@ -812,6 +813,7 @@ void * assemble_KMA_dense_threaded(void *arg) {</td>
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812
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="c"> <span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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813
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="c"> <span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="c"> <span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="c"> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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817
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="c"> <span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="c"> <span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="c"> <span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</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">@@ -986,9 +988,9 @@ void * assemble_KMA_dense_threaded(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC988" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC989" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC990" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC989" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get normed score */</span></span>
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get normed score <span class="idiff left right">check read coverage </span>*/</span></span>
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">t_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="n" style="color: #333;"><span class="idiff">qseq</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">)</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">mrc</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">t_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="n" style="color: #333;"><span class="idiff">mrc</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">qseq</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">)</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">alnStat</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">match</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC994" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">aln_len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC995" 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="LC996" class="line" lang="c"> <span class="n" style="color: #333;">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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1622,7 +1624,7 @@ void * assemble_KMA(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC1624" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">q_start</span><span class="p">,</span> <span class="n" style="color: #333;">q_end</span><span class="p">;</span></span>
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1625
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<pre style="margin: 0;"> <span id="LC1625" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qBoundPtr</span><span class="p">;</span></span>
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1626
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<pre style="margin: 0;"> <span id="LC1626" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</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;">counts</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1625" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1627" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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1626
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1628
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<pre style="margin: 0;"> <span id="LC1628" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">var</span><span class="p">,</span> <span class="n" style="color: #333;">nucHighVar</span><span class="p">;</span></span>
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1627
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1629
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<pre style="margin: 0;"> <span id="LC1629" 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;">s</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s_next</span><span class="p">;</span></span>
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1628
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1630
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<pre style="margin: 0;"> <span id="LC1630" 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;">t</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t_next</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q_next</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1654" 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="1656" 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">@@ -1654,6 +1656,7 @@ void * assemble_KMA(void *arg) {</td>
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1654
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1656
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<pre style="margin: 0;"> <span id="LC1656" class="line" lang="c"> <span class="n" style="color: #333;">delta</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;">size</span><span class="p">;</span></span>
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1655
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1657
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<pre style="margin: 0;"> <span id="LC1657" class="line" lang="c"> <span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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1656
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1658
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<pre style="margin: 0;"> <span id="LC1658" class="line" lang="c"> <span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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1659
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<pre style="margin: 0;">+<span id="LC1659" class="line" lang="c"> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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1657
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1660
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<pre style="margin: 0;"> <span id="LC1660" class="line" lang="c"> <span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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1658
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1661
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<pre style="margin: 0;"> <span id="LC1661" class="line" lang="c"> <span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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1659
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1662
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<pre style="margin: 0;"> <span id="LC1662" class="line" lang="c"> <span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</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">@@ -1857,9 +1860,9 @@ void * assemble_KMA(void *arg) {</td>
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1857
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1860
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<pre style="margin: 0;"> <span id="LC1860" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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1858
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1861
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<pre style="margin: 0;"> <span id="LC1861" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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1859
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1862
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<pre style="margin: 0;"> <span id="LC1862" class="line" lang="c"> </span>
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1860
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<pre style="margin: 0;">-<span id="LC1860" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get normed score */</span></span>
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1863
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<pre style="margin: 0;">+<span id="LC1863" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get normed score <span class="idiff left right">check read coverage </span>*/</span></span>
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1861
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1864
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<pre style="margin: 0;"> <span id="LC1864" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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1862
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<pre style="margin: 0;">-<span id="LC1862" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1865" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">aln_len</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">t_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="n" style="color: #333;"><span class="idiff">qseq</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">)</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">mrc</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">t_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="n" style="color: #333;"><span class="idiff">mrc</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">qseq</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">)</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">alnStat</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">match</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1866" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">aln_len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1867" 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="LC1868" class="line" lang="c"> <span class="n" style="color: #333;">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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,6 +79,7 @@ struct assemble_thread {</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC84" 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;">template_name</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">files</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kma (1.3.10-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Fix faulty VCS URL</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Sat, 06 Feb 2021 12:48:44 +0530</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">kma (1.3.9-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> zlib1g-dev</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/kma</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/k<span class="idiff left right">am</span>.git</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/k<span class="idiff left right">ma</span>.git</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Homepage: https://bitbucket.org/genomicepidemiology/kma</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#5bb411548ec4b39482e6de83d3ad98f29b1162b1"><strong>kma.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="158" 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">@@ -158,7 +158,8 @@ static void helpMessage(int exeStatus) {</td>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-and</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Both mrs and p_value thresholds</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">has to reached to in order to</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">report a template hit.</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">or</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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159
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-mq</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum mapping quality</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="160" 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">
160
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-mrs</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum alignment score,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">normalized to alignment length</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0.50</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-mct</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Max overlap between templates</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0.50</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-mrc</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum read coverage</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">0.10</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-mct</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Max overlap between templates</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0.10</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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162
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-reward</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Score for match</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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163
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-penalty</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for mismatch</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">-2</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-gapopen</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for gap opening</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">-3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="207" 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">@@ -206,7 +207,7 @@ int kma_main(int argc, char *argv[]) {</td>
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206
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">;</span></span>
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207
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">;</span></span>
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208
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles_PE</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles_INT</span><span class="p">,</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">coverT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">coverT</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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210
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">;</span></span>
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211
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">exe_len</span><span class="p">,</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">escape</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">step1</span><span class="p">,</span> <span class="n" style="color: #333;">step2</span><span class="p">;</span></span>
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212
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">totFrags</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="258" 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="259" 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">@@ -258,7 +259,8 @@ int kma_main(int argc, char *argv[]) {</td>
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258
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c"> <span class="n" style="color: #333;">mq</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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259
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"> <span class="n" style="color: #333;">bcd</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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260
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c"> <span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="c"> <span class="n" style="color: #333;">coverT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="c"> <span class="n" style="color: #333;">coverT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="c"> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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262
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c"> <span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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263
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c"> <span class="n" style="color: #333;">one2one</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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264
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'q'</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">@@ -686,6 +688,15 @@ int kma_main(int argc, char *argv[]) {</td>
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686
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688
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<pre style="margin: 0;"> <span id="LC688" 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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687
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689
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="c"> <span class="p">}</span></span>
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688
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690
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="c"> <span class="p">}</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-mrc"</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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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="693" 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">
693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="c"> <span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtod</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exeBasic</span><span class="p">);</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exeBasic</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Invalid argument at </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-mrc</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" 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="LC698" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="c"> <span class="p">}</span></span>
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689
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700
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-mct"</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="LC701" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span><span class="p">;</span></span>
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691
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702
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1285" 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">@@ -1274,7 +1285,7 @@ int kma_main(int argc, char *argv[]) {</td>
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1274
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1285
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<pre style="margin: 0;"> <span id="LC1285" 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;">Mt1</span><span class="p">)</span> <span class="p">{</span></span>
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1275
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1286
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<pre style="margin: 0;"> <span id="LC1286" class="line" lang="c"> <span class="n" style="color: #333;">myTemplatefilename</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;">templatefilename</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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1276
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1287
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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">templatefilename</span><span class="p">);</span></span>
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1277
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<pre style="margin: 0;">-<span id="LC1277" class="line" lang="c"> <span class="n" style="color: #333;">runKMA_Mt1</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">strjoin</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">argc</span><span class="p">),</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1288" 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">
1288
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="c"> <span class="n" style="color: #333;">runKMA_Mt1</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">strjoin</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">argc</span><span class="p">),</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1278" 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">
1278
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<td class="diff-line-num new_line" data-linenumber="1289" 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">
1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1279" 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">
1279
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<td class="diff-line-num new_line" data-linenumber="1290" 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">
1290
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<pre style="margin: 0;"> <span id="LC1290" 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;">"# Closing files</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1280" 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">
1280
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<td class="diff-line-num 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">
1291
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<pre style="margin: 0;"> <span id="LC1291" 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;">step2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1293" 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="1304" 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">@@ -1293,11 +1304,11 @@ int kma_main(int argc, char *argv[]) {</td>
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<td class="diff-line-num old_line" data-linenumber="1293" 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">
1293
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<td class="diff-line-num new_line" data-linenumber="1304" 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">
1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="c"> <span class="n" style="color: #333;">myTemplatefilename</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;">templatefilename</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1294" 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">
1294
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<td class="diff-line-num new_line" data-linenumber="1305" 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">
1305
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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">templatefilename</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1295" 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">
1295
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<td class="diff-line-num new_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1306
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">spltDB</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;">targetNum</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1296" 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">
1296
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<td class="diff-line-num new_line old" data-linenumber="1307" 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="LC1296" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">runKMA_spltDB</span><span class="p">(</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">,</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" data-linenumber="1307" 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">
1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">runKMA_spltDB</span><span class="p">(</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">,</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1297" 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">
1297
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<td class="diff-line-num new_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1308
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<pre style="margin: 0;"> <span id="LC1308" class="line" lang="c"> <span class="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;">mem_mode</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1298" 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">
1298
</td>
<td class="diff-line-num new_line old" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1298" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">runKMA_MEM</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">runKMA_MEM</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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1299
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1310
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<pre style="margin: 0;"> <span id="LC1310" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1300
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<pre style="margin: 0;">-<span id="LC1300" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">runKMA</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">runKMA</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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1312
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="c"> <span class="p">}</span></span>
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1302
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1313
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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">);</span></span>
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1303
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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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Closing files</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#088a2f1aaa170cd721dbae6f4b2bcb8239c7119a"><strong>mt1.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">@@ -80,7 +80,7 @@ void printFsa_pairMt1(Qseqs *header, Qseqs *qseq, Qseqs *header_r, Qseqs *qseq_r</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_Mt1</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_Mt1</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"> </span>
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85
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">coverScore</span><span class="p">,</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">delta</span><span class="p">;</span></span>
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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_lengths</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -290,6 +290,7 @@ void runKMA_Mt1(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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290
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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291
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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292
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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293
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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294
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="355" 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">@@ -354,6 +355,7 @@ void runKMA_Mt1(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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354
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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355
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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356
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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357
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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358
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#1046a66b72dbb642e4d57ce820566e6c09c525d9"><strong>mt1.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,4 +24,4 @@</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printFsaMt1</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printFsa_pairMt1</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_Mt1</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_Mt1</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#97e3379ce2e33418ea5b83d3faaf35326b973d41"><strong>nw.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">@@ -49,11 +49,13 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="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="LC50" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">q_len</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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="LC54" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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54
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="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="p">;</span></span>
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55
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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56
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</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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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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57
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<td class="diff-line-num new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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58
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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59
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="sc" style="color: #d14;">'_'</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" 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="64" 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">@@ -62,6 +64,7 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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62
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">);</span></span>
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63
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65
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<pre style="margin: 0;"> <span id="LC65" 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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64
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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65
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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66
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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67
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="sc" style="color: #d14;">'_'</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="248" 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="251" 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">@@ -248,6 +251,7 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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248
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="c"> <span class="n" style="color: #333;">E_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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249
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="c"> <span class="n" style="color: #333;">nuc_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t_s</span><span class="p">;</span></span>
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250
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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251
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<td class="diff-line-num new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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252
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<td class="diff-line-num new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">E_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="253" 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">
253
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<td class="diff-line-num new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nuc_pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">template_length</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="257" 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="261" 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">@@ -257,6 +261,7 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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<td class="diff-line-num old_line" data-linenumber="257" 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">
257
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<td class="diff-line-num new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getNuc</span><span class="p">(</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">nuc_pos</span><span class="p">);</span></span>
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258
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<td class="diff-line-num new_line" data-linenumber="262" 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">
262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="259" 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">
259
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<td class="diff-line-num new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">])</span> <span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'|'</span> <span class="o" style="font-weight: 600;">:</span> <span class="sc" style="color: #d14;">'_'</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" 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">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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260
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<td class="diff-line-num new_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nuc_pos</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="261" 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">
261
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<td class="diff-line-num new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">E_ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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262
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="324" 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="329" 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">@@ -324,11 +329,13 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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<td class="diff-line-num old_line" data-linenumber="324" 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">
324
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<td class="diff-line-num new_line" data-linenumber="329" 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">
329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="325" 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">
325
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<td class="diff-line-num new_line" data-linenumber="330" 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">
330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</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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<td class="diff-line-num old_line" data-linenumber="326" 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">
326
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<td class="diff-line-num new_line" data-linenumber="331" 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">
331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="332" 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">
332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="327" 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">
327
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<td class="diff-line-num new_line" data-linenumber="333" 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">
333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="328" 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">
328
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<td class="diff-line-num new_line" data-linenumber="334" 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">
334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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329
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<td class="diff-line-num new_line" data-linenumber="335" 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">
335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="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="p">;</span></span>
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330
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336
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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331
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<td class="diff-line-num new_line" data-linenumber="337" 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">
337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="338" 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">
338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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332
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<td class="diff-line-num new_line" data-linenumber="339" 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">
339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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333
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<td class="diff-line-num new_line" data-linenumber="340" 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">
340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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334
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<td class="diff-line-num new_line" data-linenumber="341" 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">
341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="sc" style="color: #d14;">'_'</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="337" 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="344" 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">@@ -337,6 +344,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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337
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<td class="diff-line-num new_line" data-linenumber="344" 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">
344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">);</span></span>
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338
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<td class="diff-line-num new_line" data-linenumber="345" 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">
345
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<pre style="margin: 0;"> <span id="LC345" 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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339
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<td class="diff-line-num new_line" data-linenumber="346" 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">
346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="347" 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">
347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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340
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<td class="diff-line-num new_line" data-linenumber="348" 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">
348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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341
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<td class="diff-line-num new_line" data-linenumber="349" 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">
349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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342
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350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="sc" style="color: #d14;">'_'</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="567" 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="575" 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">@@ -567,6 +575,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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<td class="diff-line-num old_line" data-linenumber="567" 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">
567
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<td class="diff-line-num new_line" data-linenumber="575" 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">
575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="c"> <span class="n" style="color: #333;">E_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">bq_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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568
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<td class="diff-line-num new_line" data-linenumber="576" 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">
576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="c"> <span class="n" style="color: #333;">nuc_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t_s</span><span class="p">;</span></span>
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569
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="578" 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">
578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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570
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="571" 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">
571
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<td class="diff-line-num new_line" data-linenumber="580" 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">
580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">E_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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572
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nuc_pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">template_length</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="576" 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="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -576,6 +585,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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576
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<td class="diff-line-num new_line" data-linenumber="585" 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">
585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getNuc</span><span class="p">(</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">nuc_pos</span><span class="p">);</span></span>
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577
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<td class="diff-line-num new_line" data-linenumber="586" 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">
586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">[</span><span class="n" style="color: #333;">q_pos</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="578" 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">
578
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<td class="diff-line-num new_line" data-linenumber="587" 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">
587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">])</span> <span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'|'</span> <span class="o" style="font-weight: 600;">:</span> <span class="sc" style="color: #d14;">'_'</span><span class="p">;</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="579" 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">
579
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nuc_pos</span><span class="p">;</span></span>
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580
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590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="c"> <span class="n" style="color: #333;">E_ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">bq_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="581" 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">
581
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">q_pos</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="643" 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="653" 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">@@ -643,14 +653,17 @@ AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg,</td>
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643
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653
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="644" 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">
644
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<td class="diff-line-num new_line" data-linenumber="654" 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">
654
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">q_len</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="645" 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">
645
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<td class="diff-line-num new_line" data-linenumber="655" 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">
655
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="646" 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">
646
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657
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
647
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658
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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648
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659
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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649
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<td class="diff-line-num new_line" data-linenumber="660" 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">
660
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span><span class="p">;</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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650
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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651
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663
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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652
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664
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<pre style="margin: 0;"> <span id="LC664" 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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653
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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="654" 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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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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654
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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655
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668
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="656" 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">
656
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669
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="827" 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="840" 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">@@ -827,12 +840,14 @@ AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg,</td>
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827
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840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="828" 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">
828
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<td class="diff-line-num new_line" data-linenumber="841" 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">
841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="c"> <span class="n" style="color: #333;">nuc_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t_s</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="829" 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">
829
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842
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="843" 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">
843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="830" 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">
830
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<td class="diff-line-num new_line" data-linenumber="844" 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">
844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="831" 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">
831
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<td class="diff-line-num new_line" data-linenumber="845" 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">
845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">E_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="832" 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">
832
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<td class="diff-line-num new_line" data-linenumber="846" 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">
846
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nuc_pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">template_length</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="833" 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">
833
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<td class="diff-line-num new_line" data-linenumber="847" 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">
847
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="c"> <span class="n" style="color: #333;">nuc_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="834" 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">
834
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848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="835" 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">
835
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<td class="diff-line-num new_line" data-linenumber="849" 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">
849
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">E_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="850" 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">
850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="836" 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">
836
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<td class="diff-line-num new_line" data-linenumber="851" 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">
851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nuc_pos</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="837" 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">
837
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<td class="diff-line-num new_line" data-linenumber="852" 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">
852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="c"> <span class="n" style="color: #333;">E_ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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838
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853
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="883" 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="898" 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">@@ -883,14 +898,17 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query</td>
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883
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898
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="884" 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">
884
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<td class="diff-line-num new_line" data-linenumber="899" 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">
899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">q_len</span><span class="p">)</span> <span class="p">{</span></span>
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885
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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886
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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887
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903
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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888
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904
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<pre style="margin: 0;"> <span id="LC904" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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889
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905
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="890" 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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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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890
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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<td class="diff-line-num old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
891
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="892" 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">
892
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909
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<pre style="margin: 0;"> <span id="LC909" 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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893
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910
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="894" 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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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="894" 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">
894
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912
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="895" 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">
895
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913
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="896" 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">
896
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914
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1110" 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="1128" 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">@@ -1110,12 +1128,14 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query</td>
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1110
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1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="c"> <span class="n" style="color: #333;">E_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">bq_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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1111
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1129
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<pre style="margin: 0;"> <span id="LC1129" class="line" lang="c"> <span class="n" style="color: #333;">nuc_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t_s</span><span class="p">;</span></span>
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1112
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1130
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1113
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</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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1114
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1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">E_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1115" 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">
1115
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<td class="diff-line-num new_line" data-linenumber="1134" 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">
1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nuc_pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">template_length</span><span class="p">)</span> <span class="p">{</span></span>
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1116
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1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="c"> <span class="n" style="color: #333;">nuc_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1117
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1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="c"> <span class="p">}</span></span>
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1118
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1137
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<pre style="margin: 0;"> <span id="LC1137" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">E_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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1119
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1139
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nuc_pos</span><span class="p">;</span></span>
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1120
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<td class="diff-line-num 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">
1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="c"> <span class="n" style="color: #333;">E_ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">bq_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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1121
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1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">q_pos</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,6 +37,7 @@ struct alnScore {</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC43" 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">@@ -135,7 +135,7 @@ char * nameLoad(Qseqs *name, FILE *infile) {</td>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</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;">name</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_template</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_tmp_template</span><span class="p">,</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplate</span><span class="p">,</span> <span class="n" style="color: #333;">tot</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="p">,</span> <span class="n" style="color: #333;">rand</span><span class="p">,</span> <span class="n" style="color: #333;">sparse</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="281" 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">@@ -281,6 +281,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Running KMA.</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="LC282" class="line" lang="c"> <span class="n" style="color: #333;">t0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clock</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* allocate stuff */</span></span>
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="c"> <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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286
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c"> <span class="n" style="color: #333;">alnThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="423" 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="424" 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">@@ -423,6 +424,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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423
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="c"> <span class="p">}</span></span>
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424
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"> <span class="n" style="color: #333;">kmaPipe</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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425
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="c"> </span>
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426
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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427
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="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;">1</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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428
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="c"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="488" 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="490" 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">@@ -488,6 +490,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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<td class="diff-line-num old_line" data-linenumber="488" 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">
488
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490
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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489
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<td class="diff-line-num new_line" data-linenumber="491" 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">
491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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490
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<td class="diff-line-num new_line" data-linenumber="492" 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">
492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="493" 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">
493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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491
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<td class="diff-line-num new_line" data-linenumber="494" 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">
494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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492
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<td class="diff-line-num new_line" data-linenumber="495" 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">
495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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493
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1150" 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="1153" 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">@@ -1150,6 +1153,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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1150
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<td class="diff-line-num new_line" data-linenumber="1153" 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">
1153
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<pre style="margin: 0;"> <span id="LC1153" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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1151
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1154
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<pre style="margin: 0;"> <span id="LC1154" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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1152
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1155
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<pre style="margin: 0;"> <span id="LC1155" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1156" 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">
1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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1153
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<td class="diff-line-num new_line" data-linenumber="1157" 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">
1157
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<pre style="margin: 0;"> <span id="LC1157" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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1154
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<td class="diff-line-num new_line" data-linenumber="1158" 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">
1158
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<pre style="margin: 0;"> <span id="LC1158" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1155" 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">
1155
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<td class="diff-line-num new_line" data-linenumber="1159" 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">
1159
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<pre style="margin: 0;"> <span id="LC1159" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1293" 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="1297" 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">@@ -1293,7 +1297,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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1293
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1297
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<pre style="margin: 0;"> <span id="LC1297" class="line" lang="c"> <span class="p">}</span></span>
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1294
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1298
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<pre style="margin: 0;"> <span id="LC1298" class="line" lang="c"> </span>
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1295
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<td class="diff-line-num new_line" 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="cm" style="color: #998; font-style: italic;">/* Close files */</span></span>
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1296
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<td class="diff-line-num new_line old" data-linenumber="1300" 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="LC1296" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">fclose</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">seq_in</span></span><span class="p">);</span></span>
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">close</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">seq_in_no</span></span><span class="p">);</span></span>
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1297
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1301
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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">res_out</span><span class="p">);</span></span>
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1298
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1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">alignment_out</span><span class="p">)</span> <span class="p">{</span></span>
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1299
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1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">alignment_out</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1322" 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="1326" 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">@@ -1322,7 +1326,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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1322
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1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">status</span><span class="p">;</span></span>
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1323
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1327
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<pre style="margin: 0;"> <span id="LC1327" class="line" lang="c"><span class="p">}</span></span>
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1324
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1328
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="c"></span>
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1325
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<pre style="margin: 0;">-<span id="LC1325" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_MEM</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_MEM</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* runKMA_MEM is a memory saving version of runKMA,</span></span>
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1332
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> at the cost it chooses best templates based on kmers</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2227" 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="2231" 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">@@ -2227,6 +2231,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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2227
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2231
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<pre style="margin: 0;"> <span id="LC2231" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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2228
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2232
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<pre style="margin: 0;"> <span id="LC2232" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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2229
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2233
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<pre style="margin: 0;"> <span id="LC2233" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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2234
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<pre style="margin: 0;">+<span id="LC2234" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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2235
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<pre style="margin: 0;"> <span id="LC2235" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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2236
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<pre style="margin: 0;"> <span id="LC2236" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2237" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2296" 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">@@ -2291,6 +2296,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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2291
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2296
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<pre style="margin: 0;"> <span id="LC2296" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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2297
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<pre style="margin: 0;"> <span id="LC2297" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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2298
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<pre style="margin: 0;"> <span id="LC2298" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2299" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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2300
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<pre style="margin: 0;"> <span id="LC2300" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2301" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2302" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ustrdup</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;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">load_DBs_KMA</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">infile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_MEM</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_MEM</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#3ff76aca17d9815adbbfee02596e6c4d46aa1384"><strong>sam.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">@@ -98,6 +98,7 @@ char * makeCigar(Qseqs *Cigar, const Aln *aligned) {</td>
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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="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">saminit</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</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;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">DB_size</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"@HD</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VN:1.6</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">GO:reference</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="LC102" 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><span class="n" style="color: #333;">DB_size</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"@SQ</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">SN:%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">LN:%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">),</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">template_lengths</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#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">@@ -395,7 +395,7 @@ unsigned get_ankers_spltDB(int *infoSize, int *out_Tem, CompDNA *qseq, Qseqs *he</td>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">num</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_spltDB</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_spltDB</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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399
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c"> </span>
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400
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* https://www.youtube.com/watch?v=LtXEMwSG5-8 */</span></span>
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1429" 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="1429" 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">@@ -1429,6 +1429,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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1429
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1429
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<pre style="margin: 0;"> <span id="LC1429" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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1430
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1430
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<pre style="margin: 0;"> <span id="LC1430" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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1431
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1431
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<pre style="margin: 0;"> <span id="LC1431" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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1432
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1433
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<pre style="margin: 0;"> <span id="LC1433" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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1433
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1434
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<pre style="margin: 0;"> <span id="LC1434" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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1434
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1435
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<pre style="margin: 0;"> <span id="LC1435" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1493" 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="1494" 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">@@ -1493,6 +1494,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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1493
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1494
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<pre style="margin: 0;"> <span id="LC1494" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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1494
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1495
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<pre style="margin: 0;"> <span id="LC1495" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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1495
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1496
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<pre style="margin: 0;"> <span id="LC1496" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreT</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1497" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mrc</span><span class="p">;</span></span>
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1496
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1498
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<pre style="margin: 0;"> <span id="LC1498" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1499" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1500" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#e55b6b603fd8c696cd5ece7be98d78898a9ee58f"><strong>spltdb.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">@@ -35,4 +35,4 @@ struct spltDBbuff {</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">print_ankers_spltDB</span><span class="p">(</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;">out_Tem</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rc_flag</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">print_ankers_Sparse_spltDB</span><span class="p">(</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;">out_Tem</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rc_flag</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">get_ankers_spltDB</span><span class="p">(</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;">infoSize</span><span class="p">,</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;">out_Tem</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inputfile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_spltDB</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_spltDB</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/ae65bf4d61b9d349d2bdbd6797e5e7efd35e0b24...3f30a8a2d9ec1aa92b0571c83151dc64afb8154c#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.<span class="idiff left right">9</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.<span class="idiff left right">10</span>"</span></span></pre>
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