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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/4ac3c30413e380eb61bbe03a1ecd5d8310fee40a">4ac3c304</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-02-14T20:50:41+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.11</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<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="#99bf70d606be11e0793b7e3ba6c29182326341d6">
assembly.c
</a>
</li>
<li class="file-stats">
<a href="#97e3379ce2e33418ea5b83d3faaf35326b973d41">
nw.c
</a>
</li>
<li class="file-stats">
<a href="#61a960d3b9862f2e47015c82850b2b590c708d06">
nw.h
</a>
</li>
<li class="file-stats">
<a href="#ca9efd475143efe0a1b0464c67f49900d98ca75a">
runkma.c
</a>
</li>
<li class="file-stats">
<a href="#3ff76aca17d9815adbbfee02596e6c4d46aa1384">
sam.c
</a>
</li>
<li class="file-stats">
<a href="#cd8b7c197c9ac04f72eb54b22a8a01d5b1d0391f">
sparse.c
</a>
</li>
<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
</a>
</li>
<li class="file-stats">
<a href="#0adaae20b3777809504470476732216fb88066f5">
xml.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
<a href="https://salsa.debian.org/med-team/kma/-/commit/4ac3c30413e380eb61bbe03a1ecd5d8310fee40a#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40"><strong>align.c</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -201,7 +201,8 @@ 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="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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<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>
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<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
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<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>
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<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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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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<td class="diff-line-num old old_line" data-linenumber="204" 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">
204
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<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>
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<td class="diff-line-num new old_line" data-linenumber="205" 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="204" 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">
204
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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="LC204" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="205" 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="205" 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">
205
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<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;">qGaps</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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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;">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="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="diff-line-num 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">
207
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<pre style="margin: 0;"> <span id="LC207" 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="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">
207
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208
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<pre style="margin: 0;"> <span id="LC208" 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="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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -216,7 +217,8 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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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">
217
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<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;">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="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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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;">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="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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219
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<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;">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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219
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<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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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;">tGaps</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 new new_line" data-linenumber="221" 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">
221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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220
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c"> <span class="n" style="color: #333;">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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221
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<pre style="margin: 0;"> <span id="LC223" 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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222
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224
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<pre style="margin: 0;"> <span id="LC224" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -228,7 +230,8 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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228
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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;">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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229
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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;">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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232
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<pre style="margin: 0;"> <span id="LC232" 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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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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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;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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232
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="c"> <span class="n" style="color: #333;">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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233
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">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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234
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -263,8 +266,10 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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263
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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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
264
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<td class="diff-line-num new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">))</span> <span class="p">{</span></span>
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265
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<td class="diff-line-num new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="p">{</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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267
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" 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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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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268
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c"> <span class="p">}</span></span>
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269
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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270
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="283" style="width: 35px; color: rgba(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">@@ -278,11 +283,12 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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278
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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;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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279
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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280
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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;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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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;"><span class="idiff left right">g</span>aps</span><span class="p">);</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="c"> <span 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;"><span class="idiff left right">tG</span>aps</span><span class="p">);</span></span>
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282
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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;">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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283
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c"> <span class="n" style="color: #333;">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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284
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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;">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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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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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC292" 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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287
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c"> <span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_s</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC294" 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="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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -340,7 +346,8 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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340
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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;">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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341
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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;">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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342
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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;">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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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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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;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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344
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<td class="diff-line-num new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
351
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<pre style="margin: 0;"> <span id="LC351" 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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345
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="c"> <span class="n" style="color: #333;">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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346
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353
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<pre style="margin: 0;"> <span id="LC353" 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="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="368" style="width: 35px; color: rgba(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">@@ -361,7 +368,8 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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361
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<td class="diff-line-num new_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
368
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<pre style="margin: 0;"> <span id="LC368" 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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362
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369
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<pre style="margin: 0;"> <span id="LC369" 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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363
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370
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<pre style="margin: 0;"> <span id="LC370" 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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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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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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365
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="c"> <span class="p">}</span></span>
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366
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374
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<pre style="margin: 0;"> <span id="LC374" 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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367
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="c"> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="398" style="width: 35px; color: rgba(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="406" style="width: 35px; color: rgba(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">@@ -398,8 +406,10 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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398
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="c"> <span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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399
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">))</span> <span class="p">{</span></span>
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400
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="p">{</span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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402
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="p">(</span><span class="n" style="color: #333;">Frag_align</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" 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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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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403
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="c"> <span class="p">}</span></span>
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404
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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405
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415
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<pre style="margin: 0;"> <span id="LC415" 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="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="428" style="width: 35px; color: rgba(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">@@ -418,7 +428,8 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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418
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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;">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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419
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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;">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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420
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<td class="diff-line-num new_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
430
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<pre style="margin: 0;"> <span id="LC430" 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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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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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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422
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433
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<pre style="margin: 0;"> <span id="LC433" 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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423
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434
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<pre style="margin: 0;"> <span id="LC434" 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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424
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435
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<pre style="margin: 0;"> <span id="LC435" 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="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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -569,7 +580,8 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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569
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580
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<pre style="margin: 0;"> <span id="LC580" 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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570
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581
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<pre style="margin: 0;"> <span id="LC581" 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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571
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582
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<pre style="margin: 0;"> <span id="LC582" 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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572
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<td class="diff-line-num new_line old" data-linenumber="583" 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="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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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="584" 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">
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;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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573
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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;">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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574
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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;">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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575
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587
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<pre style="margin: 0;"> <span id="LC587" 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 new_line" data-linenumber="596" style="width: 35px; color: rgba(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">@@ -584,7 +596,8 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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584
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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;">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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585
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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;">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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586
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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;">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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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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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;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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588
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601
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<pre style="margin: 0;"> <span id="LC601" 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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589
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602
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<pre style="margin: 0;"> <span id="LC602" 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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590
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603
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<pre style="margin: 0;"> <span id="LC603" 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="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="607" style="width: 35px; color: rgba(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">@@ -594,7 +607,8 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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594
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607
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<pre style="margin: 0;"> <span id="LC607" 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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595
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608
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<pre style="margin: 0;"> <span id="LC608" 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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609
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<pre style="margin: 0;"> <span id="LC609" 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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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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<pre style="margin: 0;">+<span id="LC610" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="c"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC613" 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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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -623,11 +637,12 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band_score</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat = NW_score(template_index->seq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, matrices, t_len);</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="c"> <span class="p">}</span></span>
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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;"><span class="idiff left right">g</span>aps</span><span class="p">);</span></span>
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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;">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;"><span class="idiff left right">tG</span>aps</span><span class="p">);</span></span>
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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;">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="LC642" 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="LC643" 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="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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<pre style="margin: 0;">+<span id="LC644" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC648" 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">@@ -679,7 +694,8 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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679
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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;">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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680
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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;">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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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;">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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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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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC699" 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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684
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700
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<pre style="margin: 0;"> <span id="LC700" 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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701
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -693,7 +709,8 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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693
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709
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<pre style="margin: 0;"> <span id="LC709" 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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710
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<pre style="margin: 0;"> <span id="LC710" 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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711
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<pre style="margin: 0;"> <span id="LC711" 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="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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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC715" 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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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="c"> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="727" style="width: 35px; color: rgba(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="744" style="width: 35px; color: rgba(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">@@ -727,7 +744,8 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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727
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744
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<pre style="margin: 0;"> <span id="LC744" 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="LC745" 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="LC746" 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="LC747" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="c"> </span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/4ac3c30413e380eb61bbe03a1ecd5d8310fee40a#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">@@ -34,6 +34,7 @@</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdstat.h"</span></span>
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<pre style="margin: 0;"> <span id="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 class="cp" style="color: #999; font-weight: 600;">#define mrcheck(mrc, Stat, q_len, t_len) ((mrc * q_len <= Stat.len - Stat.qGaps) || (mrc * t_len <= Stat.len - Stat.tGaps))</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="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;">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="LC40" 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">@@ -103,7 +104,8 @@ int alnFragsSE(HashMapCCI **templates_index, int *matched_templates, int *templa</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</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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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</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="LC107" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC109" 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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108
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <span class="p">}</span></span>
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="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 old_line" data-linenumber="117" style="width: 35px; color: rgba(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="119" style="width: 35px; color: rgba(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">@@ -117,9 +119,9 @@ int alnFragsSE(HashMapCCI **templates_index, int *matched_templates, int *templa</td>
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117
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<pre style="margin: 0;"> <span id="LC119" 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="LC120" 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="LC121" 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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC122" 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;"><span class="idiff left right">tG</span>aps</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;">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 class="idiff left">((</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">q_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">q_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="LC124" 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="n" style="color: #333;"><span class="idiff left">mrcheck</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q_len</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t_len</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="LC125" 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="LC126" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC127" 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">@@ -247,7 +249,8 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</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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<pre style="margin: 0;"> <span id="LC251" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</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="LC252" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"> <span 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">@@ -258,9 +261,9 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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<pre style="margin: 0;"> <span id="LC261" 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="LC262" 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="LC263" 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="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 class="idiff left">((</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_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_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="LC264" 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="n" style="color: #333;"><span class="idiff left">mrcheck</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qseq_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="n" style="color: #333;"><span class="idiff">t_len</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="LC265" 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="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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c"> <span 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;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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264
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267
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<pre style="margin: 0;"> <span id="LC267" 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_len</span><span class="p">)</span> <span class="p">{</span></span>
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265
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c"> <span class="n" style="color: #333;">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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266
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="297" style="width: 35px; color: rgba(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">@@ -294,7 +297,8 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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294
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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295
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</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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296
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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;">alnStat</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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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</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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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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298
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="c"> <span class="p">}</span></span>
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299
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c"> <span class="n" style="color: #333;">rc</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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300
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304
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<pre style="margin: 0;"> <span id="LC304" 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 old_line" data-linenumber="304" style="width: 35px; color: rgba(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="308" style="width: 35px; color: rgba(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">@@ -304,9 +308,9 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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304
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get read score */</span></span>
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305
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<pre style="margin: 0;"> <span id="LC309" 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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306
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<pre style="margin: 0;"> <span id="LC310" 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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307
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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="o" style="font-weight: 600;">&&</span> <span class="p"><span class="idiff left">((</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="LC311" 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="n" style="color: #333;"><span class="idiff left">mrcheck</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><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="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="n" style="color: #333;"><span class="idiff">t_len</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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308
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312
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<pre style="margin: 0;"> <span id="LC312" 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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309
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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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" 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;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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310
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c"> </span>
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311
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315
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<pre style="margin: 0;"> <span id="LC315" 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_len</span><span class="p">)</span> <span class="p">{</span></span>
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312
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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;">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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<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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -576,7 +580,8 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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576
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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577
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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578
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<td class="diff-line-num new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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579
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<td class="diff-line-num new_line old" data-linenumber="583" 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="LC579" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</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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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="584" 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">
584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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580
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585
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<pre style="margin: 0;"> <span id="LC585" 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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581
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586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="c"> <span class="p">}</span></span>
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582
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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="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 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="592" style="width: 35px; color: rgba(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">@@ -587,9 +592,9 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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587
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592
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<pre style="margin: 0;"> <span id="LC592" 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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588
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593
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<pre style="margin: 0;"> <span id="LC593" 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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589
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594
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<pre style="margin: 0;"> <span id="LC594" 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 class="idiff left">((</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_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_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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595
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<pre style="margin: 0;">+<span id="LC595" 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="n" style="color: #333;"><span class="idiff left">mrcheck</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qseq_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="n" style="color: #333;"><span class="idiff">t_len</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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591
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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;">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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592
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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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" 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;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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593
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="c"> </span>
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594
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599
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<pre style="margin: 0;"> <span id="LC599" 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_len</span><span class="p">)</span> <span class="p">{</span></span>
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595
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600
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<pre style="margin: 0;"> <span id="LC600" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="622" style="width: 35px; color: rgba(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">@@ -622,7 +627,8 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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622
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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;">alnStat</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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623
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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;">alnStat</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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624
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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625
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</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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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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626
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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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627
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="c"> <span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC634" 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">@@ -632,9 +638,9 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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<pre style="margin: 0;"> <span id="LC638" 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="LC639" 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="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;">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="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="o" style="font-weight: 600;">&&</span> <span class="p"><span class="idiff left">((</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="LC641" 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="n" style="color: #333;"><span class="idiff left">mrcheck</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><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="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="n" style="color: #333;"><span class="idiff">t_len</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="LC642" 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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="c"> <span class="n" style="color: #333;">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;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC645" 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_len</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="c"> <span class="n" style="color: #333;">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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -899,7 +905,8 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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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="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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<pre style="margin: 0;"> <span id="LC907" class="line" lang="c"> <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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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902
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</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="LC908" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="c"> <span class="n" style="color: #333;">alnStat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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903
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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;">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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904
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911
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="c"> <span class="p">}</span></span>
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905
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912
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<pre style="margin: 0;"> <span id="LC912" 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="914" style="width: 35px; color: rgba(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">@@ -907,7 +914,7 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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907
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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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908
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915
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="c"> </span>
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909
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916
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<pre style="margin: 0;"> <span id="LC916" 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 class="idiff left">((</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_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_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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917
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<pre style="margin: 0;">+<span id="LC917" 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="n" style="color: #333;"><span class="idiff left">mrcheck</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qseq_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="n" style="color: #333;"><span class="idiff">t_len</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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911
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918
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<pre style="margin: 0;"> <span id="LC918" 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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919
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<pre style="margin: 0;"> <span id="LC919" 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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<td class="diff-line-num old_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
913
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920
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<pre style="margin: 0;"> <span id="LC920" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* rc */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="919" style="width: 35px; color: rgba(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="926" style="width: 35px; color: rgba(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">@@ -919,7 +926,8 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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919
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926
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="c"> <span class="n" style="color: #333;">alnStat_r</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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920
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<td class="diff-line-num new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
927
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="c"> <span class="n" style="color: #333;">alnStat_r</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="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
921
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="c"> <span class="n" style="color: #333;">alnStat_r</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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922
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<pre style="margin: 0;">-<span id="LC922" class="line" lang="c"> <span class="n" style="color: #333;">alnStat_r</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="LC929" class="line" lang="c"> <span class="n" style="color: #333;">alnStat_r</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="c"> <span class="n" style="color: #333;">alnStat_r</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="c"> <span class="p">}</span></span>
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924
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="c"> <span class="n" style="color: #333;">rc</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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925
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="c"> <span class="p">}</span> <span 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 old_line" data-linenumber="927" style="width: 35px; color: rgba(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="935" style="width: 35px; color: rgba(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">@@ -927,17 +935,17 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="c"> <span class="p">}</span></span>
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928
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936
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<pre style="margin: 0;"> <span id="LC936" class="line" lang="c"> </span>
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929
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937
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<pre style="margin: 0;"> <span id="LC937" 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="LC930" 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_r</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_r</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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938
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<pre style="margin: 0;">+<span id="LC938" 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_r</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_r</span><span class="p">.</span><span class="n" style="color: #333;">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="n" style="color: #333;"><span class="idiff">mrcheck</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alnStat_r</span></span><span class="p"><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="n" style="color: #333;"><span class="idiff">t_len</span></span><span class="p"><span class="idiff right">)</span>)</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="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="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;">len</span><span class="p">;</span></span>
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932
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940
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<pre style="margin: 0;"> <span id="LC940" class="line" lang="c"> </span>
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933
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941
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<pre style="margin: 0;"> <span id="LC941" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Handle negative insertsizes caused by trimming,</span></span>
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934
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942
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> user stupidity or sample error. */</span></span>
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935
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943
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</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_r</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>
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936
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944
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<pre style="margin: 0;"> <span id="LC944" 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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937
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<td class="diff-line-num new_line old" data-linenumber="945" 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="LC937" 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_r</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_r</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_r</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" 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_r</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_r</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_r</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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938
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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 class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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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;">start</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;">pos</span><span class="p">;</span></span>
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940
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<pre style="margin: 0;">-<span id="LC940" 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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="941" 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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948
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<pre style="margin: 0;">+<span id="LC948" 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;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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941
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949
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<pre style="margin: 0;"> <span id="LC949" class="line" lang="c"> <span class="p">}</span></span>
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942
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950
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<pre style="margin: 0;"> <span id="LC950" class="line" lang="c"> </span>
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943
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951
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<pre style="margin: 0;"> <span id="LC951" 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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="961" style="width: 35px; color: rgba(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">@@ -953,7 +961,7 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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953
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="c"> <span class="p">}</span></span>
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954
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962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="c"> </span>
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955
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963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* save best match(es) */</span></span>
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956
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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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964
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<pre style="margin: 0;">+<span id="LC964" 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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957
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965
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<pre style="margin: 0;"> <span id="LC965" 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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958
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966
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<pre style="margin: 0;"> <span id="LC966" 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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959
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967
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<pre style="margin: 0;"> <span id="LC967" 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="diff-line-num unfold js-unfold old_line" data-linenumber="1117" style="width: 35px; color: rgba(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="1125" style="width: 35px; color: rgba(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">@@ -1117,7 +1125,7 @@ void * alnFrags_threaded(void * arg) {</td>
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1117
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1125
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<pre style="margin: 0;"> <span id="LC1125" 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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1118
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1126
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="c"> <span class="p">}</span></span>
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1119
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1127
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<pre style="margin: 0;"> <span id="LC1127" class="line" lang="c"> </span>
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1120
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<pre style="margin: 0;">-<span id="LC1120" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">unmapped</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sam</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2096</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 right"> </span><span class="n" style="color: #333;">unmapped</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1129" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">unmapped</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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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;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flag</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;">nibble2base</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/4ac3c30413e380eb61bbe03a1ecd5d8310fee40a#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">@@ -39,6 +39,7 @@</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdstat.h"</span></span>
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<pre style="margin: 0;"> <span id="LC40" 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="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "xml.h"</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define mrcheck(mrc, Stat, q_len, t_len) ((mrc * q_len <= Stat.len - Stat.qGaps) || (mrc * t_len <= Stat.len - Stat.tGaps))</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"></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;">void</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;">assembly_KMA_Ptr</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="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">assemble_KMA</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" 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;">significantBase</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">significantNuc</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">@@ -432,11 +433,11 @@ void * assemble_KMA_threaded(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC433" 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="LC434" 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="LC435" 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="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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC436" 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;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get normed score check read coverage */</span></span>
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<pre style="margin: 0;"> <span id="LC439" 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="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="o" style="font-weight: 600;">&&</span> <span class="p"><span class="idiff left">((</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="LC440" 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="n" style="color: #333;"><span class="idiff left">mrcheck</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><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="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="n" style="color: #333;"><span class="idiff">t_len</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="LC441" 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="LC442" 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="LC443" 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">@@ -986,11 +987,11 @@ void * assemble_KMA_dense_threaded(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC987" 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="LC988" 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="LC989" 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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC990" 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;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC991" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get normed score check read coverage */</span></span>
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<pre style="margin: 0;"> <span id="LC993" 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="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="o" style="font-weight: 600;">&&</span> <span class="p"><span class="idiff left">((</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="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="n" style="color: #333;"><span class="idiff left">mrcheck</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><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="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="n" style="color: #333;"><span class="idiff">t_len</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="LC995" 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="LC996" 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="LC997" 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">@@ -1293,7 +1294,7 @@ void * skip_assemble_KMA(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1295" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC1296" class="line" lang="c"> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cover</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="LC1296" class="line" lang="c"> <span class="n" style="color: #333;">aligned_assem</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="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exp</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">t_len</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// expected coverage from depth</span></span>
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="c"> <span class="n" style="color: #333;">aligned_assem</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;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">;</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//</span>(1 - exp((-1.0) * aligned_assem->depth / t_len)) * t_len; // expected coverage from depth</span></span>
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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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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1300
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="c"><span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1858,11 +1859,11 @@ void * assemble_KMA(void *arg) {</td>
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1859
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<pre style="margin: 0;"> <span id="LC1859" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get read score */</span></span>
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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;">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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1861
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<pre style="margin: 0;"> <span id="LC1861" 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="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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1862" 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;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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1863
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<pre style="margin: 0;"> <span id="LC1863" class="line" lang="c"> </span>
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1864
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<pre style="margin: 0;"> <span id="LC1864" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get normed score check read coverage */</span></span>
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<pre style="margin: 0;"> <span id="LC1865" 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="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="o" style="font-weight: 600;">&&</span> <span class="p"><span class="idiff left">((</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="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="n" style="color: #333;"><span class="idiff left">mrcheck</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mrc</span></span><span class="p"><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="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="n" style="color: #333;"><span class="idiff">t_len</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="LC1867" 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="LC1868" 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="LC1869" 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">@@ -50,13 +50,15 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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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="LC53" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC56" 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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<pre style="margin: 0;"> <span id="LC57" 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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<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;">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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<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;">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="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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<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;">tGaps</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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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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60
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<td class="diff-line-num new_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">
62
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<pre style="margin: 0;"> <span id="LC62" 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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61
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63
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<pre style="margin: 0;"> <span id="LC63" 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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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;">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;">q_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,7 +67,8 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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65
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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66
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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;">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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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;">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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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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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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69
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">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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70
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">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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71
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74
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<pre style="margin: 0;"> <span id="LC74" 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;">t_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -252,7 +255,8 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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252
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255
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<pre style="margin: 0;"> <span id="LC255" 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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253
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256
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<pre style="margin: 0;"> <span id="LC256" 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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257
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<pre style="margin: 0;"> <span id="LC257" 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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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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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" 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="LC259" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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256
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260
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<pre style="margin: 0;"> <span id="LC260" 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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257
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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;">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="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">
258
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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;">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 unfold js-unfold old_line" data-linenumber="273" style="width: 35px; color: rgba(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="277" style="width: 35px; color: rgba(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">@@ -273,26 +277,28 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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273
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nuc_pos</span><span class="p">;</span></span>
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274
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<td class="diff-line-num new_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">
278
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<pre style="margin: 0;"> <span id="LC278" 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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275
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC279" 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;">len</span><span class="p">;</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" 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;">qGaps</span><span class="p">;</span></span>
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276
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"> <span class="p">}</span></span>
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277
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<td class="diff-line-num new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
282
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<pre style="margin: 0;"> <span id="LC282" 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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278
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<td class="diff-line-num new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
283
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<pre style="margin: 0;"> <span id="LC283" 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="mi" style="color: #099;">5</span><span class="p">;</span></span>
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279
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<td class="diff-line-num new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
284
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<pre style="margin: 0;"> <span id="LC284" 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="sc" style="color: #d14;">'_'</span><span class="p">;</span> </span>
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280
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285
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<pre style="margin: 0;"> <span id="LC285" 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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281
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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;">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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<td class="diff-line-num new new_line" data-linenumber="287" 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">
287
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<pre style="margin: 0;">+<span id="LC287" 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;">qGaps</span><span class="p">;</span></span>
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282
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288
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<pre style="margin: 0;"> <span id="LC288" 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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<td class="diff-line-num new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
289
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<pre style="margin: 0;"> <span id="LC289" 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="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;">3</span><span class="p">))</span> <span class="p">{</span></span>
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284
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<td class="diff-line-num 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">
290
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<pre style="margin: 0;"> <span id="LC290" 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="mi" style="color: #099;">5</span><span class="p">;</span></span>
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285
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<td class="diff-line-num new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
291
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<pre style="margin: 0;"> <span id="LC291" 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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286
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292
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<pre style="margin: 0;"> <span id="LC292" 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="sc" style="color: #d14;">'_'</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC287" 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;">gaps</span><span class="p">;</span></span>
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288
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293
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<pre style="margin: 0;"> <span id="LC293" 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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289
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294
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<pre style="margin: 0;"> <span id="LC294" 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;">len</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span><span class="p">;</span></span>
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290
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c"> <span class="p">}</span></span>
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291
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297
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<pre style="margin: 0;"> <span id="LC297" 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="mi" style="color: #099;">5</span><span class="p">;</span></span>
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292
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"> <span class="n" style="color: #333;">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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293
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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;">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="sc" style="color: #d14;">'_'</span><span class="p">;</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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295
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300
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<pre style="margin: 0;"> <span id="LC300" 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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301
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<pre style="margin: 0;">+<span id="LC301" 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;">tGaps</span><span class="p">;</span></span>
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296
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="c"> <span class="p">}</span></span>
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297
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303
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<pre style="margin: 0;"> <span id="LC303" 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;">len</span><span class="p">;</span></span>
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298
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304
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<pre style="margin: 0;"> <span id="LC304" 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="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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -328,15 +334,17 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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328
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="c"> </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="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="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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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC336" 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 new old_line" data-linenumber="331" 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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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;">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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331
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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;">len</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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332
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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;">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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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;"><span class="idiff left right">g</span>aps</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="LC334" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">score</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<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;"><span class="idiff left right">tG</span>aps</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="LC341" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">qGaps</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC342" 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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<pre style="margin: 0;"> <span id="LC343" 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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<pre style="margin: 0;"> <span id="LC344" 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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<pre style="margin: 0;"> <span id="LC345" 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="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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<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;">tGaps</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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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;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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340
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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;">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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341
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349
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<pre style="margin: 0;"> <span id="LC349" 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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350
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<pre style="margin: 0;"> <span id="LC350" 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;">q_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="353" style="width: 35px; color: rgba(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">@@ -345,7 +353,8 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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<pre style="margin: 0;"> <span id="LC353" 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="LC354" 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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<pre style="margin: 0;"> <span id="LC355" 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="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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<pre style="margin: 0;">+<span id="LC356" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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349
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358
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<pre style="margin: 0;"> <span id="LC358" 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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350
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359
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<pre style="margin: 0;"> <span id="LC359" 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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351
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360
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<pre style="margin: 0;"> <span id="LC360" 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;">t_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<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">@@ -576,7 +585,8 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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576
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585
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<pre style="margin: 0;"> <span id="LC585" 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="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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;">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="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;">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 old_line" data-linenumber="579" 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">
579
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<td class="diff-line-num new_line old" data-linenumber="588" 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="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 new old_line" data-linenumber="580" 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="588" 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">
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;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="589" 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">
589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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580
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590
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<pre style="margin: 0;"> <span id="LC590" 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="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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<td class="diff-line-num new_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
591
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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;">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="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
582
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592
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<pre style="margin: 0;"> <span id="LC592" 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 unfold js-unfold old_line" data-linenumber="598" style="width: 35px; color: rgba(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="608" style="width: 35px; color: rgba(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">@@ -598,6 +608,7 @@ 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="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
598
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<td class="diff-line-num new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
608
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<pre style="margin: 0;"> <span id="LC608" 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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599
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<td class="diff-line-num new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
609
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<pre style="margin: 0;"> <span id="LC609" 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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600
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<td class="diff-line-num new_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
610
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<pre style="margin: 0;"> <span id="LC610" 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;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="611" 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">
611
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<pre style="margin: 0;">+<span id="LC611" 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;">qGaps</span><span class="p">;</span></span>
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601
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<td class="diff-line-num new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
602
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<td class="diff-line-num new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
613
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<pre style="margin: 0;"> <span id="LC613" 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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603
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<td class="diff-line-num new_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
614
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<pre style="margin: 0;"> <span id="LC614" 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="mi" style="color: #099;">5</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">@@ -605,22 +616,23 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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605
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616
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<pre style="margin: 0;"> <span id="LC616" 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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606
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="c"> <span class="n" style="color: #333;">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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607
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618
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<pre style="margin: 0;"> <span id="LC618" 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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619
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<pre style="margin: 0;">+<span id="LC619" 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;">qGaps</span><span class="p">;</span></span>
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608
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620
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<pre style="margin: 0;"> <span id="LC620" 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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609
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<td class="diff-line-num new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
621
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<pre style="margin: 0;"> <span id="LC621" 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="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;">3</span><span class="p">))</span> <span class="p">{</span></span>
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610
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622
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<pre style="margin: 0;"> <span id="LC622" 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="mi" style="color: #099;">5</span><span class="p">;</span></span>
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611
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623
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<pre style="margin: 0;"> <span id="LC623" 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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612
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624
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<pre style="margin: 0;"> <span id="LC624" 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="sc" style="color: #d14;">'_'</span><span class="p">;</span></span>
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613
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<pre style="margin: 0;">-<span id="LC613" 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;">gaps</span><span class="p">;</span></span>
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614
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625
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<pre style="margin: 0;"> <span id="LC625" 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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615
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626
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<pre style="margin: 0;"> <span id="LC626" 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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616
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627
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<pre style="margin: 0;"> <span id="LC627" 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;">len</span><span class="p">;</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" 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;">tGaps</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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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="c"> <span class="p">}</span></span>
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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;">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="mi" style="color: #099;">5</span><span class="p">;</span></span>
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619
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<td class="diff-line-num new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
631
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<pre style="margin: 0;"> <span id="LC631" 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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620
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632
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<pre style="margin: 0;"> <span id="LC632" 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="sc" style="color: #d14;">'_'</span><span class="p">;</span></span>
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621
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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622
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633
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<pre style="margin: 0;"> <span id="LC633" 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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623
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<pre style="margin: 0;"> <span id="LC634" 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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<pre style="margin: 0;">+<span id="LC635" 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;">tGaps</span><span class="p">;</span></span>
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636
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC637" 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;">len</span><span class="p">;</span></span>
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -654,17 +666,20 @@ AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg,</td>
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654
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666
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<pre style="margin: 0;"> <span id="LC666" 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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655
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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;">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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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;">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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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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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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658
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671
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<pre style="margin: 0;"> <span id="LC671" 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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659
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672
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<pre style="margin: 0;"> <span id="LC672" 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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660
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673
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<pre style="margin: 0;"> <span id="LC673" 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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674
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<pre style="margin: 0;"> <span id="LC674" 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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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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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span><span class="p">;</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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663
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677
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<pre style="margin: 0;"> <span id="LC677" 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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664
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678
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<pre style="margin: 0;"> <span id="LC678" 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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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;">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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<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;">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="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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<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;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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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;">qGaps</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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668
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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;">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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669
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684
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="c"> <span class="p">}</span></span>
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685
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<pre style="margin: 0;"> <span id="LC685" 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="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="856" style="width: 35px; color: rgba(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">@@ -841,7 +856,8 @@ AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg,</td>
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841
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856
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<pre style="margin: 0;"> <span id="LC856" 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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857
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<pre style="margin: 0;"> <span id="LC857" 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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843
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858
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<pre style="margin: 0;"> <span id="LC858" 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="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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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC861" 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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862
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<pre style="margin: 0;"> <span id="LC862" 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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<pre style="margin: 0;"> <span id="LC863" 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 unfold js-unfold old_line" data-linenumber="856" style="width: 35px; color: rgba(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">@@ -856,16 +872,18 @@ AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg,</td>
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856
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872
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<pre style="margin: 0;"> <span id="LC872" 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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857
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873
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<pre style="margin: 0;"> <span id="LC873" 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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858
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874
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<pre style="margin: 0;"> <span id="LC874" 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;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC875" 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;">qGaps</span><span class="p">;</span></span>
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859
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876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="c"> <span class="p">}</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" 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;">qGaps</span><span class="p">;</span></span>
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860
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878
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<pre style="margin: 0;"> <span id="LC878" 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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861
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879
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<pre style="margin: 0;"> <span id="LC879" 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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862
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880
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<pre style="margin: 0;"> <span id="LC880" 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 old_line" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
863
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881
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<pre style="margin: 0;"> <span id="LC881" 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="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;">3</span><span class="p">))</span> <span class="p">{</span></span>
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864
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<td class="diff-line-num new_line old" data-linenumber="882" 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="LC864" 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;">gaps</span><span class="p">;</span></span>
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865
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882
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<pre style="margin: 0;"> <span id="LC882" 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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866
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883
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<pre style="margin: 0;"> <span id="LC883" 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;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="884" 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">
884
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<pre style="margin: 0;">+<span id="LC884" 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;">tGaps</span><span class="p">;</span></span>
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867
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="c"> <span class="p">}</span></span>
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868
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<pre style="margin: 0;">-<span id="LC868" 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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="869" 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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886
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<pre style="margin: 0;">+<span id="LC886" 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;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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869
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887
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<pre style="margin: 0;"> <span id="LC887" 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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870
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888
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="c"> <span class="p">}</span></span>
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871
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<td class="diff-line-num new_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
889
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<pre style="margin: 0;"> <span id="LC889" 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;">len</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="917" style="width: 35px; color: rgba(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">@@ -899,17 +917,20 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query</td>
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899
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917
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<pre style="margin: 0;"> <span id="LC917" 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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900
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<td class="diff-line-num new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
918
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<pre style="margin: 0;"> <span id="LC918" 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="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
901
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<td class="diff-line-num new_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
919
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<pre style="margin: 0;"> <span id="LC919" 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 old_line" data-linenumber="902" 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">
902
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<td class="diff-line-num new_line old" data-linenumber="920" 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="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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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="921" 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">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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903
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922
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<pre style="margin: 0;"> <span id="LC922" 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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904
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923
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<pre style="margin: 0;"> <span id="LC923" 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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905
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<td class="diff-line-num new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
924
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<pre style="margin: 0;"> <span id="LC924" 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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906
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925
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<pre style="margin: 0;"> <span id="LC925" 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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907
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<td class="diff-line-num new_line old" data-linenumber="926" 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="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 new old_line" data-linenumber="908" 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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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="927" 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">
927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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908
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<td class="diff-line-num new_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
928
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<pre style="margin: 0;"> <span id="LC928" 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="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
909
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929
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<pre style="margin: 0;"> <span id="LC929" 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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910
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930
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<pre style="margin: 0;"> <span id="LC930" 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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911
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931
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<pre style="margin: 0;"> <span id="LC931" 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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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 new old_line" data-linenumber="913" 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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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="913" 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="933" 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">
933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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913
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<td class="diff-line-num new_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
934
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<pre style="margin: 0;"> <span id="LC934" 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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914
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="c"> <span class="p">}</span></span>
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915
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936
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<pre style="margin: 0;"> <span id="LC936" 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="1129" style="width: 35px; color: rgba(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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1129,7 +1150,8 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query</td>
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<td class="diff-line-num old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1129
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1150
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<pre style="margin: 0;"> <span id="LC1150" 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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1130
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1151
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<pre style="margin: 0;"> <span id="LC1151" 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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1152
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<pre style="margin: 0;"> <span id="LC1152" 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 old_line" data-linenumber="1132" 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">
1132
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<td class="diff-line-num new_line old" data-linenumber="1153" 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="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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<td class="diff-line-num new old_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1153" 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">
1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">tGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1154" 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">
1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">qGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1133
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC1155" 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="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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<td class="diff-line-num new_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1156
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<pre style="margin: 0;"> <span id="LC1156" 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="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1135
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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="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 unfold js-unfold old_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1167" style="width: 35px; color: rgba(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">@@ -1145,18 +1167,20 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query</td>
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1145
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<td class="diff-line-num new_line" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1167
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<pre style="margin: 0;"> <span id="LC1167" 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="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1146
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<td class="diff-line-num new_line" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1168
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<pre style="margin: 0;"> <span id="LC1168" 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 old_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1147
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<td class="diff-line-num new_line" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1169
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<pre style="margin: 0;"> <span id="LC1169" 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;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1170" 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">
1170
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<pre style="margin: 0;">+<span id="LC1170" 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;">qGaps</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1148
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<td class="diff-line-num new_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1171
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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1149" 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="1172" 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">
1172
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<pre style="margin: 0;">+<span id="LC1172" 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;">qGaps</span><span class="p">;</span></span>
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1149
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<td class="diff-line-num new_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1173
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<pre style="margin: 0;"> <span id="LC1173" 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="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">
1150
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<td class="diff-line-num new_line" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1174
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<pre style="margin: 0;"> <span id="LC1174" 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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1151
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<td class="diff-line-num new_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1175
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<pre style="margin: 0;"> <span id="LC1175" 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 old_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1152
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<td class="diff-line-num new_line" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1176
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<pre style="margin: 0;"> <span id="LC1176" 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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1153
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<td class="diff-line-num new_line" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1177
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<pre style="margin: 0;"> <span id="LC1177" 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="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;">3</span><span class="p">))</span> <span class="p">{</span></span>
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1154
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<td class="diff-line-num new_line old" data-linenumber="1178" 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="LC1154" 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;">gaps</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="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1178
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<pre style="margin: 0;"> <span id="LC1178" 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 old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1156
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<td class="diff-line-num new_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1179
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<pre style="margin: 0;"> <span id="LC1179" 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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<pre style="margin: 0;"> <span id="LC1180" 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;">len</span><span class="p">;</span></span>
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1181
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<pre style="margin: 0;">+<span id="LC1181" 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;">tGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1182" class="line" lang="c"> <span class="p">}</span></span>
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1159
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<pre style="margin: 0;">-<span id="LC1159" 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;"><span class="idiff left right">g</span>aps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1183" 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;"><span class="idiff left right">tG</span>aps</span><span class="p">;</span></span>
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1160
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1184
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<pre style="margin: 0;"> <span id="LC1184" 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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1161
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1185
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<pre style="margin: 0;"> <span id="LC1185" 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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1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/4ac3c30413e380eb61bbe03a1ecd5d8310fee40a#61a960d3b9862f2e47015c82850b2b590c708d06"><strong>nw.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +38,8 @@ struct alnScore {</td>
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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="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tGaps</span><span class="p">;</span></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;">qGaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">aln</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/4ac3c30413e380eb61bbe03a1ecd5d8310fee40a#ca9efd475143efe0a1b0464c67f49900d98ca75a"><strong>runkma.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -335,7 +335,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_lengths</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="LC336" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">templates_index</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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<pre style="margin: 0;"> <span id="LC337" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</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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<pre style="margin: 0;">-<span id="LC338" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</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="p">(</span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="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;">alnThread</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;"><span class="idiff left">sam</span></span><span class="p"><span class="idiff">;</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//</span>(sam == 1) ? 1 : 0;</span></span>
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339
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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;">alnThread</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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340
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnThreads</span><span class="p">;</span></span>
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<td class="diff-line-num old_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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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="c"> <span class="n" style="color: #333;">alnThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnThread</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="405" style="width: 35px; color: rgba(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="405" style="width: 35px; color: rgba(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">@@ -405,7 +405,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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<td class="diff-line-num old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
405
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</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;">kmersize</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
406
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<td class="diff-line-num new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</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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407
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</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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408
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<td class="diff-line-num new_line old" data-linenumber="408" 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="LC408" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</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="p">(</span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="408" 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">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</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;"><span class="idiff left">sam</span></span><span class="p"><span class="idiff">;</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//</span>(sam == 1) ? 1 : 0;</span></span>
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409
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<td class="diff-line-num new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</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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410
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_lengths</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="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
411
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="c"> <span class="n" style="color: #333;">alnThread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">templates_index</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1258" style="width: 35px; color: rgba(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="1258" style="width: 35px; color: rgba(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">@@ -1258,11 +1258,11 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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1258
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1258
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<pre style="margin: 0;"> <span id="LC1258" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1259
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<td class="diff-line-num new_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1259
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<pre style="margin: 0;"> <span id="LC1259" class="line" lang="c"> <span class="p">}</span></span>
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1260
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<td class="diff-line-num new_line" data-linenumber="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1260
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<pre style="margin: 0;"> <span id="LC1260" 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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1261
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<td class="diff-line-num new_line old" data-linenumber="1261" 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="LC1261" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">sam</span></span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">sam</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sam</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2096</span></span><span class="p"><span class="idiff right">))</span></span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1262
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<pre style="margin: 0;"> <span id="LC1262" 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;">template_index</span> <span class="o" style="font-weight: 600;">=</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>
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<pre style="margin: 0;"> <span id="LC1263" 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;">template_name</span> <span class="o" style="font-weight: 600;">=</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>
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1264
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<pre style="margin: 0;"> <span id="LC1264" 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;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1265" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">assembly_KMA_Ptr</span></span><span class="p">(</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">skip_assemble_KMA</span></span><span class="p">(</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//skip_assemble_KMA(template, sam, t_len, thread->template_name, fileCount, template_fragments, aligned_assem, qseq, header);</span></span>
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1268
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1268
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="c"> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">depth</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">@@ -2424,7 +2424,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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<pre style="margin: 0;"> <span id="LC2424" class="line" lang="c"> <span class="p">}</span></span>
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2425
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<pre style="margin: 0;"> <span id="LC2425" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2426" 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="LC2427" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">sam</span></span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2427" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">sam</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sam</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2096</span></span><span class="p"><span class="idiff right">))</span></span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2428" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* load DB */</span></span>
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<pre style="margin: 0;"> <span id="LC2429" class="line" lang="c"> <span class="n" style="color: #333;">seq_seeker</span> <span class="o" style="font-weight: 600;">*=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2430" class="line" lang="c"> <span class="n" style="color: #333;">lseek</span><span class="p">(</span><span class="n" style="color: #333;">seq_in_no</span><span class="p">,</span> <span class="n" style="color: #333;">seq_seeker</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/4ac3c30413e380eb61bbe03a1ecd5d8310fee40a#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">@@ -142,7 +142,6 @@ int samwrite(const Qseqs *qseq, const Qseqs *header, const Qseqs *Qual, char *rn</td>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 2048 supplementary alignment</span></span>
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<pre style="margin: 0;"> <span id="LC143" 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="LC144" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c"> </span>
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146
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">qname</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">header</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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147
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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148
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Qual</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="150" style="width: 35px; color: rgba(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="149" style="width: 35px; color: rgba(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">@@ -150,6 +149,7 @@ int samwrite(const Qseqs *qseq, const Qseqs *header, const Qseqs *Qual, char *rn</td>
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150
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149
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<pre style="margin: 0;"> <span id="LC149" 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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151
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"*"</span><span class="p">;</span></span>
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152
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"> <span class="p">}</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"> </span>
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="p">)</span> <span class="p">{</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"> <span class="n" style="color: #333;">mapQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">254</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;">mapQ</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">254</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;">mapQ</span><span class="p">;</span></span>
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155
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"> <span class="n" style="color: #333;">et</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stats</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" style="width: 35px; color: rgba(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="172" style="width: 35px; color: rgba(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">@@ -172,11 +172,11 @@ int samwrite(const Qseqs *qseq, const Qseqs *header, const Qseqs *Qual, char *rn</td>
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> <span class="p">}</span></span>
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">rnext</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"*"</span><span class="p">;</span></span>
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">pnext</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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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c"> </span>
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176
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">tab</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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177
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qname</span><span class="p">)</span> <span class="p">{</span></span>
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178
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<pre style="margin: 0;"> <span id="LC177" 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;">qname</span><span class="p">)</span> <span class="p">{</span></span>
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179
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178
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<pre style="margin: 0;"> <span id="LC178" 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;">qname</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">)</span> <span class="p">{</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">tab</span><span class="p">;</span></span>
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qname</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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181
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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182
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qname</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">@@ -192,15 +192,16 @@ int samwrite(const Qseqs *qseq, const Qseqs *header, const Qseqs *Qual, char *rn</td>
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192
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c"> <span class="p">}</span></span>
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193
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193
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<pre style="margin: 0;"> <span id="LC193" 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="p">)</span> <span class="p">{</span></span>
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"> <span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">makeCigar</span><span class="p">(</span><span class="n" style="color: #333;">Cigar</span><span class="p">,</span> <span class="n" style="color: #333;">aligned</span><span class="p">);</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">Cigar</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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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="s" style="color: #d14;">"%dS"</span><span class="p">,</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="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)))));</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">Cigar</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="LC197" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="s" style="color: #d14;">"%dS"</span><span class="p">,</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="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)))));</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <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;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ET:i:%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">AS:i:%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;">qname</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">rname</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">mapQ</span><span class="p">,</span> <span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">rnext</span><span class="p">,</span> <span class="n" style="color: #333;">pnext</span><span class="p">,</span> <span class="n" style="color: #333;">tlen</span><span class="p">,</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;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">et</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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200
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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201
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">)</span> <span class="p">{</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">qname</span><span class="p">[</span><span class="n" style="color: #333;">tab</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">qname</span><span class="p">[</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-</span></span><span class="n" style="color: #333;">tab</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>
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204
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <span class="p">}</span></span>
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> </span>
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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;">return</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/4ac3c30413e380eb61bbe03a1ecd5d8310fee40a#cd8b7c197c9ac04f72eb54b22a8a01d5b1d0391f"><strong>sparse.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">@@ -153,8 +153,12 @@ char ** load_DBs_Sparse(char *templatefilename, unsigned **template_lengths, uns</td>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> </span>
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154
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* load lengths */</span></span>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">DB_file</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c"> <span class="n" style="color: #333;">fread</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 class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">DB_file</span><span class="p">);</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="c"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_ulengths</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="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">DB_file</span><span class="p">);</span> </span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fread</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 class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">DB_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_ulengths</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="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">DB_file</span><span class="p">);</span> </span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c"> <span class="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;">i</span><span class="p">)</span> <span class="p">{</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="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;">"DB needs to sparse indexed, to run a sparse mapping.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" 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="LC161" class="line" lang="c"> <span class="p">}</span></span>
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158
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c"> <span class="p">}</span></span>
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159
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"> <span class="n" style="color: #333;">templatefilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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160
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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;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">DB_file</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/4ac3c30413e380eb61bbe03a1ecd5d8310fee40a#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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17
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17
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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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18
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18
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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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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.1<span class="idiff left right">0</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.1<span class="idiff left right">1</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/4ac3c30413e380eb61bbe03a1ecd5d8310fee40a#0adaae20b3777809504470476732216fb88066f5"><strong>xml.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">@@ -212,7 +212,7 @@ void hitXML(FILE *out, const int template, const char *template_name, const Aln</td>
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212
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;"><Hsp_query-from>%d</Hsp_query-from></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">((</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">16</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;">end</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;">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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213
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;"><Hsp_query-to>%d</Hsp_query-to></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">((</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">16</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;">start</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;">end</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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214
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;"><Hsp_hit-from>%d</Hsp_hit-from></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;">alnStat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</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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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;"><Hsp_hit-to>%d</Hsp_hit-to></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;">alnStat</span><span class="o" style="font-weight: 600;">-></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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnStat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">g</span>aps</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;"><Hsp_hit-to>%d</Hsp_hit-to></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;">alnStat</span><span class="o" style="font-weight: 600;">-></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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnStat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">tG</span>aps</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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216
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;"><Hsp_query-frame>%d</Hsp_query-frame></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;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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217
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;"><Hsp_hit-frame>%d</Hsp_hit-frame></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;">alnStat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<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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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;"><Hsp_identity>%d</Hsp_identity></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;">Ms</span><span class="p">);</span></span>
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