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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/fbe9dfdc5b4c63157d8e24f78bdb0fd124f573bd">fbe9dfdc</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-06-24T23:58:21+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.22</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/c6ca158d177bda4ecf67ebe5c3fc884d814823a4">c6ca158d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-06-24T23:58:23+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.3.22'
Update to upstream version '1.3.22'
with Debian dir a9ae491615bb04fe711e05050d0ad01aafb6419b</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/115e50ac8a9e1dfbfe5628197123dc239cc756de">115e50ac</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-06-24T18:34:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef">049fadc4</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-06-24T18:34:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
</li>
</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1ff221cada819d34daa6f89593fc3d48f1acc3ce">
KMAspecification.pdf
</a>
</li>
<li class="file-stats">
<a href="#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
align.c
</a>
</li>
<li class="file-stats">
<a href="#99bf70d606be11e0793b7e3ba6c29182326341d6">
assembly.c
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#a888ec8a19e2a0e07f82fa32481af66145f2a181">
debian/kma.1
</a>
</li>
<li class="file-stats">
<a href="#51702657d9880c43fadc322e37ff105d9816cb1b">
debian/kma_index.1
</a>
</li>
<li class="file-stats">
<a href="#b1e78e83886eae054a88c729cd12b63c3bf7b4ca">
debian/kma_shm.1
</a>
</li>
<li class="file-stats">
<a href="#5bb411548ec4b39482e6de83d3ad98f29b1162b1">
kma.c
</a>
</li>
<li class="file-stats">
<a href="#ca9efd475143efe0a1b0464c67f49900d98ca75a">
runkma.c
</a>
</li>
<li class="file-stats">
<a href="#f9ead8e7fb7b1680f786604627e0ac2147f4b7ef">
savekmers.c
</a>
</li>
<li class="file-stats">
<a href="#f80652dda49a7117428c0f92935664fc8cd4e2d1">
spltdb.c
</a>
</li>
<li class="file-stats">
<a href="#f568890dac40d04b36ce5786c44ac5704d31fe78">
updateindex.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>
<li class="file-stats">
<a href="#dbf6fe29c92e85979d7bcdcde40617d9fcc417d0">
xml.h
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="1ff221cada819d34daa6f89593fc3d48f1acc3ce">
<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#1ff221cada819d34daa6f89593fc3d48f1acc3ce"><strong>KMAspecification.pdf</strong></a>
<hr>
No preview for this file type
<br>
</li>
<li id="ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40"><strong>align.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="634" style="width: 35px; color: rgba(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="634" style="width: 35px; color: rgba(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">@@ -634,7 +634,6 @@ AlnScore KMA_score(const HashMapCCI *template_index, const unsigned char *qseq,</td>
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634
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
635
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
636
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<td class="new_line diff-line-num" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
636
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="c"> <span class="n" style="color: #333;">mapQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
637
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<td class="new_line diff-line-num old" data-linenumber="637" style="width: 35px; color: rgba(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="LC637" class="line" lang="c"> </span>
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638
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<td class="new_line diff-line-num" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
637
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mem_count</span><span class="p">)</span> <span class="p">{</span></span>
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639
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<td class="new_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mem_count</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
640
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639
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="807" style="width: 35px; color: rgba(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="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -807,7 +806,7 @@ int anker_rc(const HashMapCCI *template_index, unsigned char *qseq, int q_len, i</td>
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807
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_start</span><span class="p">;</span></span>
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808
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="c"> <span class="n" style="color: #333;">q_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q_end</span><span class="p">;</span></span>
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809
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808
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="c"> <span class="n" style="color: #333;">q_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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810
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_start</span><span class="p">;</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_start</span><span class="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">q_start</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">preseed</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">template_index</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="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q_end</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_start</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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811
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">q_start</span><span class="p">)</span> <span class="p">{</span></span>
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812
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_start</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC812" 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">@@ -957,7 +956,7 @@ int anker_rc(const HashMapCCI *template_index, unsigned char *qseq, int q_len, i</td>
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="c"> <span class="p">}</span></span>
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC960" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">one2one</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</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>
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">one2one</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><span class="idiff left"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kmersize</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">bestScore</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</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;">bestScore</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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962
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<pre style="margin: 0;"> <span id="LC961" 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="LC962" 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;">bestScore</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1141,7 +1140,7 @@ int anker_rc_comp(const HashMapCCI *template_index, unsigned char *qseq, unsigne</td>
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1141
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="c"> <span class="p">}</span></span>
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1142
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC1144" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">one2one</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</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>
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">one2one</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><span class="idiff left"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kmersize</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">bestScore</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">q_len</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;">bestScore</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1145" 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="LC1146" 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;">bestScore</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#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">@@ -1055,7 +1055,7 @@ void * assemble_KMA_dense_threaded(void *arg) {</td>
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1055
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1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="c"> <span class="p">}</span></span>
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1056
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1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="c"> </span>
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1057
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1057
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">xml_out</span><span class="p">)</span> <span class="p">{</span></span>
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1058
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<td class="new_line diff-line-num old" data-linenumber="1058" style="width: 35px; color: rgba(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="LC1058" class="line" lang="c"> <span class="n" style="color: #333;">hitXML</span><span class="p">(</span><span class="n" style="color: #333;">xml_out</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">template_name</span></span><span class="p">,</span> <span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alnStat</span><span class="p">,</span> <span class="n" style="color: #333;">NWmatrices</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="c"> <span class="n" style="color: #333;">hitXML</span><span class="p">(</span><span class="n" style="color: #333;">xml_out</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">seq</span></span><span class="p">,</span> <span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alnStat</span><span class="p">,</span> <span class="n" style="color: #333;">NWmatrices</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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1059
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1059
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="c"> <span class="p">}</span></span>
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1060
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1060
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<pre style="margin: 0;"> <span id="LC1060" 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;">sam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">2096</span><span class="p">))</span> <span class="p">{</span></span>
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1061
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1061
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<pre style="margin: 0;"> <span id="LC1061" 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;">read_score</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1717" style="width: 35px; color: rgba(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="1717" style="width: 35px; color: rgba(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">@@ -1717,6 +1717,7 @@ void * assemble_KMA(void *arg) {</td>
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1717
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1717
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<pre style="margin: 0;"> <span id="LC1717" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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1718
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1718
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<pre style="margin: 0;"> <span id="LC1718" class="line" lang="c"> <span class="n" style="color: #333;">load</span> <span class="o" style="font-weight: 600;">=</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;">len</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1719
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1719
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<pre style="margin: 0;"> <span id="LC1719" class="line" lang="c"> <span class="n" style="color: #333;">matrix</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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1720
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<pre style="margin: 0;">+<span id="LC1720" class="line" lang="c"> <span class="n" style="color: #333;">seq_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq_in</span><span class="p">;</span></span>
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1720
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1721
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<pre style="margin: 0;"> <span id="LC1721" class="line" lang="c"> </span>
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1721
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1722
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<pre style="margin: 0;"> <span id="LC1722" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* start threads */</span></span>
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1722
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1723
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<pre style="margin: 0;"> <span id="LC1723" 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;">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 unfold js-unfold old_line" data-linenumber="1931" style="width: 35px; color: rgba(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="1932" style="width: 35px; color: rgba(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">@@ -1931,7 +1932,7 @@ void * assemble_KMA(void *arg) {</td>
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1931
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1932
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<pre style="margin: 0;"> <span id="LC1932" class="line" lang="c"> <span class="p">}</span></span>
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1932
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1933
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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="c"> </span>
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1933
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1934
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<pre style="margin: 0;"> <span id="LC1934" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">xml_out</span><span class="p">)</span> <span class="p">{</span></span>
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1934
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<pre style="margin: 0;">-<span id="LC1934" class="line" lang="c"> <span class="n" style="color: #333;">hitXML</span><span class="p">(</span><span class="n" style="color: #333;">xml_out</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">template_name</span></span><span class="p">,</span> <span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alnStat</span><span class="p">,</span> <span class="n" style="color: #333;">NWmatrices</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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1935
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<pre style="margin: 0;">+<span id="LC1935" class="line" lang="c"> <span class="n" style="color: #333;">hitXML</span><span class="p">(</span><span class="n" style="color: #333;">xml_out</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">seq</span></span><span class="p">,</span> <span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alnStat</span><span class="p">,</span> <span class="n" style="color: #333;">NWmatrices</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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1935
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<pre style="margin: 0;"> <span id="LC1936" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1937" 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;">sam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">2096</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1938" 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;">read_score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">kma (1.3.<span class="idiff left right">19</span>-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kma (1.3.<span class="idiff left right">22</span>-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * New upstream version 1.3.<span class="idiff left right">19</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version 1.3.<span class="idiff left right">22</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * d/*.1: Update Manpages</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * d/p/blhc.patch: Propagate hardening flags to fix blhc</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> <span class="idiff left right">Sat, 01 May 2021 22:20:10</span> +0530</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> <span class="idiff left right">Thu, 24 Jun 2021 23:59:48</span> +0530</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">kma (1.3.10-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH KMA "1" "<span class="idiff left">May</span> 2021" "kma 1.3.<span class="idiff right">19</span>" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH KMA "1" "<span class="idiff left">June</span> 2021" "kma 1.3.<span class="idiff right">22</span>" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">kma \- maps and/or aligns raw reads to a template database</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">KMA\-1.3.<span class="idiff left right">19</span> maps and/or aligns raw reads to a template database.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">KMA\-1.3.<span class="idiff left right">22</span> maps and/or aligns raw reads to a template database.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Options:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Desc: Default:</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH KMA_INDEX "1" "<span class="idiff left">May</span> 2021" "kma_index 1.3.<span class="idiff right">19</span>" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH KMA_INDEX "1" "<span class="idiff left">June</span> 2021" "kma_index 1.3.<span class="idiff right">22</span>" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">kma_index \- creates the databases needed to run KMA, from a list of fasta files given</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#b1e78e83886eae054a88c729cd12b63c3bf7b4ca"><strong>debian/kma_shm.1</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH KMA_SHM "1" "<span class="idiff left">May</span> 2021" "kma_shm 1.3.<span class="idiff right">19</span>" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH KMA_SHM "1" "<span class="idiff left">June</span> 2021" "kma_shm 1.3.<span class="idiff right">22</span>" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">kma_shm \- sets up a shared database (sysV) for mapping with KMA</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#5bb411548ec4b39482e6de83d3ad98f29b1162b1"><strong>kma.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1301" style="width: 35px; color: rgba(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">@@ -1301,7 +1301,6 @@ int kma_main(int argc, char *argv[]) {</td>
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1301
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1301
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<pre style="margin: 0;"> <span id="LC1301" 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="LC1302" class="line" lang="c"> <span class="n" style="color: #333;">myTemplatefilename</span> <span 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="LC1303" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1304" class="line" lang="c"> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="c"> <span class="n" style="color: #333;">totFrags</span> <span 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="LC1305" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* SE */</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#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">@@ -206,6 +206,9 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c"> <span class="n" style="color: #333;">alignLoadPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignLoad_fly</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC209" 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;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c"> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">=</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="LC211" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">||</span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC214" 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">@@ -1399,6 +1402,9 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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<pre style="margin: 0;"> <span id="LC1402" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC1403" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* load databases */</span></span>
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<pre style="margin: 0;"> <span id="LC1404" class="line" lang="c"> <span class="n" style="color: #333;">alignLoadPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignLoad_fly_mem</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1405" 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;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="c"> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">=</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="LC1407" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">||</span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="c"> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1410" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#f9ead8e7fb7b1680f786604627e0ac2147f4b7ef"><strong>savekmers.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">@@ -408,12 +408,26 @@ static int clearScore(int *bestTemplates, int *Score) {</td>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">testVal</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC416" 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;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC417" 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;">values_s</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">template</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">get_kmers_for_pair</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">extendScore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* save_kmers find ankering k-mers the in query sequence,</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> and is the time determining step */</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">HIT</span><span class="p">,</span> <span class="n" style="color: #333;">gaps</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">Us</span><span class="p">,</span> <span class="n" style="color: #333;">W1s</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">SU</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hitCounter</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeqCount</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hitCounter</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeqCount</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mm</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bests</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="478" style="width: 35px; color: rgba(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">@@ -478,157 +492,132 @@ int get_kmers_for_pair(const HashMapKMA *templates, const Penalties *rewards, in</td>
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478
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashMap_get</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">getKmer</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;">j</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">))))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC495" 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="LC496" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps == 0 -> Match</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps == kmersize -> 1 MM</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> kmersize < gaps -> several mismatches or indel(s)</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps < kmersize -> deletion</span></span>
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<pre style="margin: 0;">+<span id="LC500" 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="LC501" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC504" 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;">gaps</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* snp */</span></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="c"> <span class="n" style="color: #333;">gaps</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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<pre style="margin: 0;">-<span id="LC484" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* go for best scenario */</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC488" 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="LC489" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">MM</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;">gaps</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="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="LC491" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC508" 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;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mismatch or insersion */</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* adjust for consecutive k-mer mismatches */</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span 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="LC515" 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="LC496" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</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;">mm</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC498" 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;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC502" 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="LC503" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="c"> </span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* evaluate best option */</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</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;">gaps</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 class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mm</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">m</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC526" 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="LC527" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</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;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*else {</span></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // unlikely deletion or random k-mer mismatch, </span></span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // assume better and go random zero score</span></span>
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<pre style="margin: 0;">+<span id="LC533" 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="LC534" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="c"> <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="LC537" 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="LC538" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="c"> <span class="n" style="color: #333;">HIT</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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<pre style="margin: 0;">-<span id="LC511" 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="LC512" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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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<pre style="margin: 0;">-<span id="LC513" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="c"> <span class="n" style="color: #333;">l</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;">values_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC518" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="c"> <span class="n" style="color: #333;">Scores</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</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="LC525" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">M</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC531" 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="LC532" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</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="LC533" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</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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<pre style="margin: 0;">-<span id="LC534" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="c"> <span class="p">}</span> <span 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;">Scores</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="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="LC536" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">MMs</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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="LC543" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">Ms</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC546" 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="LC547" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="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="LC552" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bests</span><span class="p">]</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="LC554" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC557" 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="LC558" class="line" lang="c"> <span class="n" style="color: #333;">l</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;">last</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="LC559" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="c"> <span class="n" style="color: #333;">Scores</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="c"> </span>
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564
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</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="LC566" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])])</span> <span class="p">{</span></span>
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569
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">M</span><span class="p">;</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</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;">values_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</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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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="c"> <span class="p">}</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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="LC548" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Scores</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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 class="p">{</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">M</span><span class="p">;</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" 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;">gaps</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* snp */</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" 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;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mismatch or insersion */</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* adjust for consecutive k-mer mismatches */</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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571
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<pre style="margin: 0;"> <span id="LC569" 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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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</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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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</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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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</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;">mm</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="c"> <span class="p">}</span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" 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;">Scores</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">extendScore</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;">j</span><span class="p">))</span> <span class="p">{</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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579
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<td class="new_line diff-line-num old" data-linenumber="575" style="width: 35px; color: rgba(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;">Scores</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;">MMs</span><span class="p">;</span></span>
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580
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<pre style="margin: 0;">-<span id="LC580" 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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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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582
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<td class="new_line diff-line-num old" data-linenumber="575" style="width: 35px; color: rgba(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="LC582" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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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583
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<td class="new_line diff-line-num old" data-linenumber="575" style="width: 35px; color: rgba(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="LC583" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">Ms</span><span class="p">;</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="c"> <span class="p">}</span></span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* evaluate best option */</span></span>
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</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;">gaps</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 class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">))</span> <span class="p">{</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC579" 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="LC587" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="c"> <span class="p">}</span></span>
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589
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<pre style="margin: 0;">-<span id="LC589" 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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590
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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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;">include</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="mi" style="color: #099;">0</span><span class="p">)</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;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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593
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bests</span><span class="p">]</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="LC580" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</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;">gaps</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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<pre style="margin: 0;"> <span id="LC581" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*else {</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // unlikely deletion or random k-mer mismatch, </span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // assume better and go random zero score</span></span>
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<pre style="margin: 0;">+<span id="LC585" 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="LC586" 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="LC587" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="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="LC589" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bests</span><span class="p">]</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="LC591" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC598" 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;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="c"> <span class="n" style="color: #333;">Scores</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</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="LC606" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bests</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC594" 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="LC609" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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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;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</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;">Scores</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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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;">Scores</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;">Ms</span><span class="p">;</span></span>
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613
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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;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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614
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</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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615
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604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="c"> <span class="p">}</span></span>
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616
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bests</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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617
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="c"> <span class="p">}</span></span>
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618
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="c"> </span>
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619
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">j</span></span><span class="p">;</span></span>
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620
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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;">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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621
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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622
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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623
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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;">Us</span> <span 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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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="c"> <span class="n" style="color: #333;">W1s</span> <span 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;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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626
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="c"> <span class="p">}</span></span>
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627
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615
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">hitCounter</span><span class="p">;</span></span>
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628
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616
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<pre style="margin: 0;"> <span id="LC616" 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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629
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="c"> <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="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">+=</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;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gap over N's */</span></span>
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC623" 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">@@ -638,12 +627,12 @@ int get_kmers_for_pair(const HashMapKMA *templates, const Penalties *rewards, in</td>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</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="n" style="color: #333;">l</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;">values_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC629" 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;">l</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="n" style="color: #333;">Scores</span><span class="p">[</span><span class="n" style="color: #333;">values_s</span><span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">l</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;">score</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;">Scores</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;">values_s</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="c"> <span class="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="LC633" class="line" lang="c"> <span class="n" style="color: #333;">l</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;">last</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="LC634" 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;">l</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;">Scores</span><span class="p">[</span><span class="n" style="color: #333;">last</span><span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">l</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;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">last</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="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="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bests</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -940,7 +929,7 @@ int get_kmers_for_pair_Sparse(const HashMapKMA *templates, const Penalties *rewa</td>
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">get_kmers_for_pair_pseoudoSparse</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">extendScore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">)</span> <span class="p">{</span></span>
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941
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="c"> </span>
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942
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<td class="new_line diff-line-num" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">hitCounter</span><span class="p">,</span> <span class="n" style="color: #333;">gaps</span><span class="p">,</span> <span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">Us</span><span class="p">,</span> <span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
943
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<td class="new_line diff-line-num old" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC943" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">HIT</span><span class="p">,</span> <span class="n" style="color: #333;">SU</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bests</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">HIT</span><span class="p">,</span> <span class="n" style="color: #333;">SU</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">m</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bests</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">;</span></span>
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944
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shifter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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945
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">include</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1001" style="width: 35px; color: rgba(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">@@ -1001,159 +990,135 @@ int get_kmers_for_pair_pseoudoSparse(const HashMapKMA *templates, const Penaltie</td>
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1001
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990
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<pre style="margin: 0;"> <span id="LC990" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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1002
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991
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<pre style="margin: 0;"> <span id="LC991" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashMap_get</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">getKmer</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;">j</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">))))</span> <span class="p">{</span></span>
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1003
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992
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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1004
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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993
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<pre style="margin: 0;">+<span id="LC993" 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="LC994" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps == 0 -> Match</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps == kmersize -> 1 MM</span></span>
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> kmersize < gaps -> several mismatches or indel(s)</span></span>
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps < kmersize -> deletion</span></span>
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<pre style="margin: 0;">+<span id="LC998" 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="LC999" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" 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;">gaps</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* snp */</span></span>
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1005
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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1006
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="c"> <span class="n" style="color: #333;">gaps</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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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* go for best scenario */</span></span>
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1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1011
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<pre style="margin: 0;">-<span id="LC1011" 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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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1013
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<pre style="margin: 0;">-<span id="LC1013" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">MM</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;">gaps</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1014
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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1015
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<pre style="margin: 0;">-<span id="LC1015" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1016" class="line" lang="c"> <span class="p">}</span></span>
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1017
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<pre style="margin: 0;">-<span id="LC1017" class="line" lang="c"> <span class="p">}</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="c"> <span class="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;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mismatch or insersion */</span></span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* adjust for consecutive k-mer mismatches */</span></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1018
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1013
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<pre style="margin: 0;"> <span id="LC1013" 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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1019
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<pre style="margin: 0;">-<span id="LC1019" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</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;">mm</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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1020
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1018
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<pre style="margin: 0;"> <span id="LC1018" class="line" lang="c"> <span class="p">}</span></span>
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1021
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<pre style="margin: 0;">-<span id="LC1021" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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1022
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<pre style="margin: 0;">-<span id="LC1022" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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1023
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<pre style="margin: 0;">-<span id="LC1023" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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1024
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<pre style="margin: 0;">-<span id="LC1024" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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1025
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<pre style="margin: 0;">-<span id="LC1025" 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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1026
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<pre style="margin: 0;">-<span id="LC1026" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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1027
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<pre style="margin: 0;">-<span id="LC1027" class="line" lang="c"> <span class="p">}</span></span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* evaluate best option */</span></span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</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;">gaps</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 class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mm</span><span class="p">;</span></span>
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1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">m</span><span class="p">;</span></span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" 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="new_line diff-line-num new" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</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;">1</span><span class="p">);</span></span>
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1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="c"> <span class="p">}</span></span>
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1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*else {</span></span>
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1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // unlikely deletion or random k-mer mismatch, </span></span>
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1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // assume better and go random zero score</span></span>
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1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="c"> </span>
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1028
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1033
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<pre style="margin: 0;"> <span id="LC1033" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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1029
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1034
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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="c"> <span class="n" style="color: #333;">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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1030
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1035
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<pre style="margin: 0;"> <span id="LC1035" 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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1031
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1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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1032
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<pre style="margin: 0;">-<span id="LC1032" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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1033
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<pre style="margin: 0;">-<span id="LC1033" class="line" lang="c"> <span class="n" style="color: #333;">HIT</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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1034
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<pre style="margin: 0;">-<span id="LC1034" 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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1035
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<pre style="margin: 0;">-<span id="LC1035" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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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1036
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<pre style="margin: 0;">-<span id="LC1036" class="line" lang="c"> <span class="p">}</span></span>
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1037
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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1038" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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1039
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<pre style="margin: 0;">-<span id="LC1039" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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1040
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<pre style="margin: 0;">-<span id="LC1040" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</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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1041
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<pre style="margin: 0;">-<span id="LC1041" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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1042
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<pre style="margin: 0;">-<span id="LC1042" class="line" lang="c"> <span class="n" style="color: #333;">Scores</span><span class="p">[</span><span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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1043
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<pre style="margin: 0;">-<span id="LC1043" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HIT</span><span class="p">;</span></span>
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1044
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<pre style="margin: 0;">-<span id="LC1044" class="line" lang="c"> <span class="p">}</span></span>
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1045
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<td class="new_line diff-line-num old" data-linenumber="1038" style="width: 35px; color: rgba(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="LC1045" 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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1046
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<pre style="margin: 0;">-<span id="LC1046" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</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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1047
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<pre style="margin: 0;">-<span id="LC1047" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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1048
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<pre style="margin: 0;">-<span id="LC1048" class="line" lang="c"> <span class="n" style="color: #333;">Scores</span><span class="p">[</span><span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">last</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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1049
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<pre style="margin: 0;">-<span id="LC1049" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HIT</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1050" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</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;">values_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</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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1040
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<pre style="margin: 0;">+<span id="LC1040" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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1051
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1044
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<pre style="margin: 0;"> <span id="LC1044" class="line" lang="c"> <span class="p">}</span></span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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="new_line diff-line-num new" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1052
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<td class="new_line diff-line-num" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1047
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1053
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1053" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</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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1054
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1054" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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1055
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1055" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1056
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1056" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</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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1057
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1057" 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;">n</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1058
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1058" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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1059
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1059" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">])</span> <span class="p">{</span></span>
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1060
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1060" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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1061
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1061" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">M</span><span class="p">;</span></span>
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1062
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1062" 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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1063
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1063" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</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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1064
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1064" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</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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1065
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1065" class="line" lang="c"> <span class="p">}</span></span>
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1066
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1066" 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;">Scores</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1067
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1067" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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1068
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1068" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">extendScore</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;">j</span><span class="p">))</span> <span class="p">{</span></span>
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1069
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<pre style="margin: 0;">-<span id="LC1069" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1070
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1070" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">MMs</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1071
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1071" 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="old_line diff-line-num old" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1072
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1072" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1073
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1073" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1074
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1074" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">Ms</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1075
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1075" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1076
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1076" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1077
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1077" 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="old_line diff-line-num old" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1078
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1078" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">MM</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1079
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1079" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1080
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1080" 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="old_line diff-line-num old" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1081
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1081" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1082
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1082" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1083
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1083" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1084
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1084" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bests</span><span class="p">]</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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<td class="old_line diff-line-num old" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1085
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1085" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1086
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1086" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1087
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1087" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1088
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1088" 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="old_line diff-line-num old" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1089
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1089" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1090
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<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(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="LC1090" 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;">n</span><span class="p">)</span> <span class="p">{</span></span>
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1091
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<pre style="margin: 0;">-<span id="LC1091" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1092
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<pre style="margin: 0;">-<span id="LC1092" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">])</span> <span class="p">{</span></span>
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1093
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<pre style="margin: 0;">-<span id="LC1093" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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1094
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<pre style="margin: 0;">-<span id="LC1094" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">M</span><span class="p">;</span></span>
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1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1051
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<pre style="margin: 0;">+<span id="LC1051" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Scores</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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 class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">M</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1058
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<pre style="margin: 0;">+<span id="LC1058" 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;">gaps</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* snp */</span></span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1061
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<pre style="margin: 0;">+<span id="LC1061" 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;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mismatch or insersion */</span></span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* adjust for consecutive k-mer mismatches */</span></span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1095
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1067
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<pre style="margin: 0;"> <span id="LC1067" 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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1096
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<td class="new_line diff-line-num old" data-linenumber="1068" style="width: 35px; color: rgba(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="LC1096" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</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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1097
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<td class="new_line diff-line-num old" data-linenumber="1068" style="width: 35px; color: rgba(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="LC1097" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</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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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</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;">mm</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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1098
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1072
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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="c"> <span class="p">}</span></span>
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1099
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<td class="new_line diff-line-num old" data-linenumber="1073" style="width: 35px; color: rgba(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="LC1099" 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;">Scores</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1100
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<pre style="margin: 0;">-<span id="LC1100" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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1101
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<pre style="margin: 0;">-<span id="LC1101" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">extendScore</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;">j</span><span class="p">))</span> <span class="p">{</span></span>
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1102
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<pre style="margin: 0;">-<span id="LC1102" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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1103
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<pre style="margin: 0;">-<span id="LC1103" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">MMs</span><span class="p">;</span></span>
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1104
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<pre style="margin: 0;">-<span id="LC1104" 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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1105
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<pre style="margin: 0;">-<span id="LC1105" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1106
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<pre style="margin: 0;">-<span id="LC1106" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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="LC1107" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">Ms</span><span class="p">;</span></span>
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1108
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<pre style="margin: 0;">-<span id="LC1108" class="line" lang="c"> <span class="p">}</span></span>
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1109
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<pre style="margin: 0;">-<span id="LC1109" class="line" lang="c"> <span class="p">}</span></span>
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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="c"> </span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* evaluate best option */</span></span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</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;">gaps</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 class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">))</span> <span class="p">{</span></span>
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1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">);</span></span>
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1110
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1077
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<pre style="margin: 0;"> <span id="LC1077" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1111
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<pre style="margin: 0;">-<span id="LC1111" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">MM</span><span class="p">;</span></span>
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1112
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<pre style="margin: 0;">-<span id="LC1112" class="line" lang="c"> <span class="p">}</span></span>
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1113
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<pre style="margin: 0;">-<span id="LC1113" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1114
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<pre style="margin: 0;">-<span id="LC1114" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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1115
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<pre style="margin: 0;">-<span id="LC1115" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1116
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<pre style="margin: 0;">-<span id="LC1116" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1117
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<pre style="margin: 0;">-<span id="LC1117" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bests</span><span class="p">]</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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1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</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;">gaps</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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1118
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1079
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="c"> <span class="p">}</span></span>
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1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*else {</span></span>
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1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // unlikely deletion or random k-mer mismatch, </span></span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // assume better and go random zero score</span></span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1084
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<pre style="margin: 0;">+<span id="LC1084" 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="new_line diff-line-num new" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="c"> <span class="n" style="color: #333;">Scores</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;">score</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bests</span><span class="p">]</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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1119
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1089
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="c"> <span class="p">}</span></span>
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1120
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1090
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<pre style="margin: 0;"> <span id="LC1090" class="line" lang="c"> <span class="p">}</span></span>
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1121
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1091
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="c"> <span class="p">}</span></span>
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1122
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<td class="new_line diff-line-num old" data-linenumber="1092" style="width: 35px; color: rgba(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="LC1122" 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;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1123
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<pre style="margin: 0;">-<span id="LC1123" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1124
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<pre style="margin: 0;">-<span id="LC1124" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</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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1125
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<td class="new_line diff-line-num old" data-linenumber="1092" style="width: 35px; color: rgba(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="LC1125" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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1126
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<td class="new_line diff-line-num old" data-linenumber="1092" style="width: 35px; color: rgba(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="LC1126" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bests</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1127
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<pre style="margin: 0;">-<span id="LC1127" class="line" lang="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;">n</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1128
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<td class="new_line diff-line-num old" data-linenumber="1092" style="width: 35px; color: rgba(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="LC1128" class="line" lang="c"> <span class="n" style="color: #333;">Scores</span><span class="p">[</span><span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1129
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<td class="new_line diff-line-num old" data-linenumber="1092" style="width: 35px; color: rgba(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="LC1129" class="line" lang="c"> <span class="n" style="color: #333;">include</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1130
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<td class="new_line diff-line-num old" data-linenumber="1092" style="width: 35px; color: rgba(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="LC1130" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bests</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;">values_s</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1131
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<td class="new_line diff-line-num old" data-linenumber="1092" style="width: 35px; color: rgba(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="LC1131" class="line" lang="c"> <span class="p">}</span></span>
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1132
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<td class="new_line diff-line-num" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1092
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<pre style="margin: 0;"> <span id="LC1092" 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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1133
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<td class="new_line diff-line-num old" data-linenumber="1093" style="width: 35px; color: rgba(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="LC1133" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1134
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1096
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<pre style="margin: 0;"> <span id="LC1096" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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1135
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<pre style="margin: 0;">-<span id="LC1135" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">bests</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span></span></span>
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1136
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<td class="new_line diff-line-num old" data-linenumber="1097" style="width: 35px; color: rgba(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="LC1136" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">while</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">--</span></span><span class="n" style="color: #333;"><span class="idiff">n</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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1137
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<td class="new_line diff-line-num old" data-linenumber="1097" style="width: 35px; color: rgba(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="LC1137" class="line" lang="c"> <span class="n" style="color: #333;">Scores</span><span class="p">[</span><span class="o" style="font-weight: 600;"><span class="idiff left">*++</span></span><span class="n" style="color: #333;"><span class="idiff right">last</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1138
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<td class="new_line diff-line-num old" data-linenumber="1097" style="width: 35px; color: rgba(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="LC1138" class="line" lang="c"> <span class="n" style="color: #333;">include</span><span class="p">[</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff right">last</span></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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1139
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<td class="new_line diff-line-num old" data-linenumber="1097" style="width: 35px; color: rgba(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="LC1139" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="o" style="font-weight: 600;"><span class="idiff left">++*</span></span><span class="n" style="color: #333;"><span class="idiff">bests</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="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">last</span></span><span class="p">;</span></span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">l</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">l</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">n</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="n" style="color: #333;"><span class="idiff">l</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">template</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">SU</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="n" style="color: #333;"><span class="idiff">values_s</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="n" style="color: #333;"><span class="idiff">values</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="c"> <span class="n" style="color: #333;">Scores</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">template</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="c"> <span class="n" style="color: #333;">include</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">template</span></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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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">l</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">template</span></span><span class="p">;</span></span>
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1140
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1102
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="c"> <span class="p">}</span></span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bests</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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1141
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<td class="new_line diff-line-num" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="c"> <span class="p">}</span></span>
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1142
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<td class="new_line diff-line-num old" data-linenumber="1105" style="width: 35px; color: rgba(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="LC1142" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="c"> </span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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1143
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1107
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<pre style="margin: 0;"> <span id="LC1107" class="line" lang="c"> <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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1144
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1108
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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1145
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1109
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1146
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1110
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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1147
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1111
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="c"> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1148
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<td class="new_line diff-line-num old" data-linenumber="1112" style="width: 35px; color: rgba(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="LC1148" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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1149
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1112
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<pre style="margin: 0;"> <span id="LC1112" class="line" lang="c"> <span class="p">}</span></span>
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1150
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1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">hitCounter</span><span class="p">;</span></span>
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1151
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1114
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<pre style="margin: 0;"> <span id="LC1114" 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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1152
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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1153
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="c"> <span class="p">}</span></span>
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1154
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1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="c"> <span class="p">}</span></span>
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1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">+=</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;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gap over N's */</span></span>
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1155
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1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1156
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1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="c"> <span class="p">}</span></span>
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1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="c"> </span>
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1157
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1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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1158
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1123
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<pre style="margin: 0;"> <span id="LC1123" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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1159
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1124
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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">SU</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="2019" style="width: 35px; color: rgba(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="1984" style="width: 35px; color: rgba(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">@@ -2019,7 +1984,7 @@ int save_kmers_Sparse(const HashMapKMA *templates, const Penalties *rewards, int</td>
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2019
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1984
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<pre style="margin: 0;"> <span id="LC1984" class="line" lang="c"> <span class="p">}</span></span>
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2020
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1985
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<pre style="margin: 0;"> <span id="LC1985" class="line" lang="c"> </span>
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2021
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1986
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<pre style="margin: 0;"> <span id="LC1986" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2022
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<td class="new_line diff-line-num old" data-linenumber="1987" style="width: 35px; color: rgba(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="LC2022" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&&</span></span> <span class="n" style="color: #333;">bestScore</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;">end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1987
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<pre style="margin: 0;">+<span id="LC1987" 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">kmersize</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;">bestScore</span> <span class="o" style="font-weight: 600;"><span class="idiff right">||</span></span> <span class="n" style="color: #333;">bestScore</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;">end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2023
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<td class="new_line diff-line-num" data-linenumber="1988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1988
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<pre style="margin: 0;"> <span id="LC1988" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2024
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<td class="new_line diff-line-num" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1989
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<pre style="margin: 0;"> <span id="LC1989" 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;">deConPrintPtr</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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2025
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<td class="new_line diff-line-num" data-linenumber="1990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1990
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<pre style="margin: 0;"> <span id="LC1990" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2031" style="width: 35px; color: rgba(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="1996" style="width: 35px; color: rgba(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">@@ -2031,8 +1996,7 @@ int save_kmers_Sparse(const HashMapKMA *templates, const Penalties *rewards, int</td>
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<td class="old_line diff-line-num" data-linenumber="2031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2031
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<td class="new_line diff-line-num" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1996
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<pre style="margin: 0;"> <span id="LC1996" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">save_kmers_pseuodeSparse</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">extendScore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2032
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<td class="new_line diff-line-num" data-linenumber="1997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1997
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<pre style="margin: 0;"> <span id="LC1997" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="2033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2033
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<td class="new_line diff-line-num" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1998
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<pre style="margin: 0;"> <span id="LC1998" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">hitCounter</span><span class="p">,</span> <span class="n" style="color: #333;">gaps</span><span class="p">,</span> <span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">Us</span><span class="p">,</span> <span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2034
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<td class="new_line diff-line-num old" data-linenumber="1999" style="width: 35px; color: rgba(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="LC2034" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">HIT</span><span class="p">,</span> <span class="n" style="color: #333;">SU</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2035
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<td class="new_line diff-line-num old" data-linenumber="1999" style="width: 35px; color: rgba(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="LC2035" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1999
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<pre style="margin: 0;">+<span id="LC1999" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">HIT</span><span class="p">,</span> <span class="n" style="color: #333;">SU</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2036
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<td class="new_line diff-line-num" data-linenumber="2000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2000
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<pre style="margin: 0;"> <span id="LC2000" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shifter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2037
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<td class="new_line diff-line-num" data-linenumber="2001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2001
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<pre style="margin: 0;"> <span id="LC2001" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2038
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<td class="new_line diff-line-num" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2002
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<pre style="margin: 0;"> <span id="LC2002" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">include</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2083" style="width: 35px; color: rgba(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="2047" style="width: 35px; color: rgba(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">@@ -2083,156 +2047,132 @@ int save_kmers_pseuodeSparse(const HashMapKMA *templates, const Penalties *rewar</td>
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2083
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<td class="new_line diff-line-num" data-linenumber="2047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2047
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<pre style="margin: 0;"> <span id="LC2047" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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2084
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2048
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<pre style="margin: 0;"> <span id="LC2048" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashMap_get</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">getKmer</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;">j</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">))))</span> <span class="p">{</span></span>
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2085
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2049
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<pre style="margin: 0;"> <span id="LC2049" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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2086
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<pre style="margin: 0;">-<span id="LC2086" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2050
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<pre style="margin: 0;">+<span id="LC2050" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2051
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<pre style="margin: 0;">+<span id="LC2051" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps == 0 -> Match</span></span>
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2052
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<pre style="margin: 0;">+<span id="LC2052" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps == kmersize -> 1 MM</span></span>
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2053
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<pre style="margin: 0;">+<span id="LC2053" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> kmersize < gaps -> several mismatches or indel(s)</span></span>
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2054
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<pre style="margin: 0;">+<span id="LC2054" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps < kmersize -> deletion</span></span>
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2055
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<pre style="margin: 0;">+<span id="LC2055" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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2056
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<pre style="margin: 0;">+<span id="LC2056" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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 class="p">{</span></span>
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2057
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<pre style="margin: 0;">+<span id="LC2057" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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2058
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<pre style="margin: 0;">+<span id="LC2058" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2059
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<pre style="margin: 0;">+<span id="LC2059" 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;">gaps</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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2060
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<pre style="margin: 0;">+<span id="LC2060" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* snp */</span></span>
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2087
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2061
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<pre style="margin: 0;"> <span id="LC2061" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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2088
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<pre style="margin: 0;">-<span id="LC2088" class="line" lang="c"> <span class="n" style="color: #333;">gaps</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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2089
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<pre style="margin: 0;">-<span id="LC2089" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2090
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<pre style="margin: 0;">-<span id="LC2090" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* go for best scenario */</span></span>
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2091
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<pre style="margin: 0;">-<span id="LC2091" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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2092
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<pre style="margin: 0;">-<span id="LC2092" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2093
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<pre style="margin: 0;">-<span id="LC2093" 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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2094
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<pre style="margin: 0;">-<span id="LC2094" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2095
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<pre style="margin: 0;">-<span id="LC2095" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">MM</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;">gaps</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2096
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<pre style="margin: 0;">-<span id="LC2096" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2097
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<td class="new_line diff-line-num old" data-linenumber="2062" style="width: 35px; color: rgba(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="LC2097" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2098
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<pre style="margin: 0;">-<span id="LC2098" class="line" lang="c"> <span class="p">}</span></span>
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2099
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<pre style="margin: 0;">-<span id="LC2099" class="line" lang="c"> <span class="p">}</span></span>
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2062
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<pre style="margin: 0;">+<span id="LC2062" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2063
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<pre style="margin: 0;">+<span id="LC2063" 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;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2064
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<pre style="margin: 0;">+<span id="LC2064" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mismatch or insersion */</span></span>
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2065
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<pre style="margin: 0;">+<span id="LC2065" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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2066
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<pre style="margin: 0;">+<span id="LC2066" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* adjust for consecutive k-mer mismatches */</span></span>
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2067
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<pre style="margin: 0;">+<span id="LC2067" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2068
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<pre style="margin: 0;">+<span id="LC2068" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2069
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<pre style="margin: 0;">+<span id="LC2069" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2100
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2070
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<pre style="margin: 0;"> <span id="LC2070" 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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2101
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<pre style="margin: 0;">-<span id="LC2101" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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2071
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<pre style="margin: 0;">+<span id="LC2071" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2072
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<pre style="margin: 0;">+<span id="LC2072" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2073
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<pre style="margin: 0;">+<span id="LC2073" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</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;">mm</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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2074
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<pre style="margin: 0;">+<span id="LC2074" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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2102
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2075
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<pre style="margin: 0;"> <span id="LC2075" class="line" lang="c"> <span class="p">}</span></span>
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2103
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<pre style="margin: 0;">-<span id="LC2103" 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;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2104
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<pre style="margin: 0;">-<span id="LC2104" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2105
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<pre style="margin: 0;">-<span id="LC2105" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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2106
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<pre style="margin: 0;">-<span id="LC2106" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2107
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<pre style="margin: 0;">-<span id="LC2107" 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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2108
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<pre style="margin: 0;">-<span id="LC2108" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2109
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<pre style="margin: 0;">-<span id="LC2109" class="line" lang="c"> <span class="p">}</span></span>
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2076
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<pre style="margin: 0;">+<span id="LC2076" class="line" lang="c"> </span>
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2077
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<pre style="margin: 0;">+<span id="LC2077" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* evaluate best option */</span></span>
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2078
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<pre style="margin: 0;">+<span id="LC2078" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</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;">gaps</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 class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">))</span> <span class="p">{</span></span>
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2079
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<pre style="margin: 0;">+<span id="LC2079" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mm</span><span class="p">;</span></span>
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2080
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<pre style="margin: 0;">+<span id="LC2080" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">m</span><span class="p">;</span></span>
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2081
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<pre style="margin: 0;">+<span id="LC2081" 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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2082
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<pre style="margin: 0;">+<span id="LC2082" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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2083
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<pre style="margin: 0;">+<span id="LC2083" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</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;">1</span><span class="p">);</span></span>
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2084
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<pre style="margin: 0;">+<span id="LC2084" class="line" lang="c"> <span class="p">}</span></span>
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2085
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<pre style="margin: 0;">+<span id="LC2085" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*else {</span></span>
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2086
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<pre style="margin: 0;">+<span id="LC2086" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // unlikely deletion or random k-mer mismatch, </span></span>
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2087
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<pre style="margin: 0;">+<span id="LC2087" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // assume better and go random zero score</span></span>
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2088
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<pre style="margin: 0;">+<span id="LC2088" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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2089
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<pre style="margin: 0;">+<span id="LC2089" class="line" lang="c"> </span>
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2110
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2090
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<pre style="margin: 0;"> <span id="LC2090" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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2111
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2091
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<pre style="margin: 0;"> <span id="LC2091" class="line" lang="c"> <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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2112
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2092
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<pre style="margin: 0;"> <span id="LC2092" 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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2113
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2093
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<pre style="margin: 0;"> <span id="LC2093" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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2114
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<td class="new_line diff-line-num old" data-linenumber="2094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2114" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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2115
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<td class="new_line diff-line-num old" data-linenumber="2094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2115" class="line" lang="c"> <span class="n" style="color: #333;">HIT</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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2116
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<pre style="margin: 0;">-<span id="LC2116" 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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2117
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<td class="new_line diff-line-num old" data-linenumber="2094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2117" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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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2118
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<td class="new_line diff-line-num old" data-linenumber="2094" style="width: 35px; color: rgba(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="LC2118" class="line" lang="c"> <span class="p">}</span></span>
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2119
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2094
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<pre style="margin: 0;"> <span id="LC2094" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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2120
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<pre style="margin: 0;">-<span id="LC2120" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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2121
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<td class="new_line diff-line-num old" data-linenumber="2095" style="width: 35px; color: rgba(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="LC2121" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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2122
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<pre style="margin: 0;">-<span id="LC2122" class="line" lang="c"> <span class="n" style="color: #333;">l</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;">values_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2123
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<pre style="margin: 0;">-<span id="LC2123" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2124
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<pre style="margin: 0;">-<span id="LC2124" class="line" lang="c"> <span class="n" style="color: #333;">Score</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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2125
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<pre style="margin: 0;">-<span id="LC2125" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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2126
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<pre style="margin: 0;">-<span id="LC2126" class="line" lang="c"> <span class="p">}</span></span>
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2127
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<td class="new_line diff-line-num old" data-linenumber="2095" style="width: 35px; color: rgba(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="LC2127" 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="old_line diff-line-num old" data-linenumber="2128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2128
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<td class="new_line diff-line-num old" data-linenumber="2095" style="width: 35px; color: rgba(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="LC2128" class="line" lang="c"> <span class="n" style="color: #333;">l</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;">last</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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2129
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<pre style="margin: 0;">-<span id="LC2129" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2130
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<pre style="margin: 0;">-<span id="LC2130" class="line" lang="c"> <span class="n" style="color: #333;">Score</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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2131
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<pre style="margin: 0;">-<span id="LC2131" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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2132
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<pre style="margin: 0;">-<span id="LC2132" class="line" lang="c"> <span class="p">}</span></span>
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2095
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<pre style="margin: 0;">+<span id="LC2095" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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2096
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<pre style="margin: 0;">+<span id="LC2096" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</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;">values_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</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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2097
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<pre style="margin: 0;">+<span id="LC2097" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2098
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<pre style="margin: 0;">+<span id="LC2098" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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2099
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<pre style="margin: 0;">+<span id="LC2099" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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2100
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<pre style="margin: 0;">+<span id="LC2100" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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2133
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2101
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<pre style="margin: 0;"> <span id="LC2101" class="line" lang="c"> <span class="p">}</span></span>
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2134
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<pre style="margin: 0;">-<span id="LC2134" class="line" lang="c"> </span>
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2102
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<pre style="margin: 0;">+<span id="LC2102" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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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2103
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<pre style="margin: 0;">+<span id="LC2103" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2135
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2104
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<pre style="margin: 0;"> <span id="LC2104" class="line" lang="c"> <span class="n" style="color: #333;">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;">M</span><span class="p">;</span></span>
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2136
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<pre style="margin: 0;">-<span id="LC2136" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</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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2137
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<pre style="margin: 0;">-<span id="LC2137" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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2138
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<pre style="margin: 0;">-<span id="LC2138" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2139
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<pre style="margin: 0;">-<span id="LC2139" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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2140
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<pre style="margin: 0;">-<span id="LC2140" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2141
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<pre style="margin: 0;">-<span id="LC2141" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])])</span> <span class="p">{</span></span>
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2142
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<pre style="margin: 0;">-<span id="LC2142" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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2143
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<pre style="margin: 0;">-<span id="LC2143" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">M</span><span class="p">;</span></span>
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2144
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<pre style="margin: 0;">-<span id="LC2144" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2145
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2145" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</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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2146
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2146" class="line" lang="c"> <span class="n" style="color: #333;">Score</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="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</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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2147
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2147" class="line" lang="c"> <span class="p">}</span></span>
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2148
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2148" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Score</span><span class="p">[</span><span class="n" style="color: #333;">template</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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2149
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2149" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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2150
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2150" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">extendScore</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;">j</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2151
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2151" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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2152
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2152" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">MMs</span><span class="p">;</span></span>
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2153
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2153" 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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2154
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2154" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2155
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2155" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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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2156
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2156" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">Ms</span><span class="p">;</span></span>
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2157
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<pre style="margin: 0;">-<span id="LC2157" class="line" lang="c"> <span class="p">}</span></span>
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2158
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<pre style="margin: 0;">-<span id="LC2158" class="line" lang="c"> <span class="p">}</span></span>
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2159
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2159" 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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2160
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2160" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">MM</span><span class="p">;</span></span>
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2161
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<pre style="margin: 0;">-<span id="LC2161" class="line" lang="c"> <span class="p">}</span></span>
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2162
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2162" 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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2163
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<pre style="margin: 0;">-<span id="LC2163" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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2164
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<pre style="margin: 0;">-<span id="LC2164" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2165
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<pre style="margin: 0;">-<span id="LC2165" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2166
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<pre style="margin: 0;">-<span id="LC2166" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">]</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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2167
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<pre style="margin: 0;">-<span id="LC2167" class="line" lang="c"> <span class="p">}</span></span>
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2168
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<pre style="margin: 0;">-<span id="LC2168" class="line" lang="c"> <span class="p">}</span></span>
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2169
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<pre style="margin: 0;">-<span id="LC2169" class="line" lang="c"> <span class="p">}</span></span>
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2170
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2170" 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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2171
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2171" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2172
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<pre style="margin: 0;">-<span id="LC2172" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2173
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<pre style="margin: 0;">-<span id="LC2173" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])])</span> <span class="p">{</span></span>
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2174
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<pre style="margin: 0;">-<span id="LC2174" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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2175
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<td class="new_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(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="LC2175" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">M</span><span class="p">;</span></span>
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2105
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<pre style="margin: 0;">+<span id="LC2105" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2106
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<pre style="margin: 0;">+<span id="LC2106" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2107
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<pre style="margin: 0;">+<span id="LC2107" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2108
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<pre style="margin: 0;">+<span id="LC2108" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2109
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<pre style="margin: 0;">+<span id="LC2109" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2110
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<pre style="margin: 0;">+<span id="LC2110" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Score</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2111
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<pre style="margin: 0;">+<span id="LC2111" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2112
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<pre style="margin: 0;">+<span id="LC2112" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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 class="p">{</span></span>
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2113
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<pre style="margin: 0;">+<span id="LC2113" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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2114
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<pre style="margin: 0;">+<span id="LC2114" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">M</span><span class="p">;</span></span>
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2115
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<pre style="margin: 0;">+<span id="LC2115" 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;">gaps</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2116
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<pre style="margin: 0;">+<span id="LC2116" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* snp */</span></span>
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2117
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<pre style="margin: 0;">+<span id="LC2117" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2118
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<pre style="margin: 0;">+<span id="LC2118" 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;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2119
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<pre style="margin: 0;">+<span id="LC2119" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mismatch or insersion */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2120
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<pre style="margin: 0;">+<span id="LC2120" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* adjust for consecutive k-mer mismatches */</span></span>
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2121
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<pre style="margin: 0;">+<span id="LC2121" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2122
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<pre style="margin: 0;">+<span id="LC2122" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2123
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<pre style="margin: 0;">+<span id="LC2123" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2176
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2124
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<pre style="margin: 0;"> <span id="LC2124" 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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2177
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<td class="new_line diff-line-num old" data-linenumber="2125" style="width: 35px; color: rgba(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="LC2177" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</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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2178
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<pre style="margin: 0;">-<span id="LC2178" class="line" lang="c"> <span class="n" style="color: #333;">Score</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="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</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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2125
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<pre style="margin: 0;">+<span id="LC2125" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2126
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<pre style="margin: 0;">+<span id="LC2126" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2127
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<pre style="margin: 0;">+<span id="LC2127" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</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;">mm</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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2128
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<pre style="margin: 0;">+<span id="LC2128" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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2179
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2129
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<pre style="margin: 0;"> <span id="LC2129" class="line" lang="c"> <span class="p">}</span></span>
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2180
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<td class="new_line diff-line-num old" data-linenumber="2130" style="width: 35px; color: rgba(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="LC2180" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Score</span><span class="p">[</span><span class="n" style="color: #333;">template</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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2181
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<pre style="margin: 0;">-<span id="LC2181" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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2182
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<pre style="margin: 0;">-<span id="LC2182" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">extendScore</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;">j</span><span class="p">))</span> <span class="p">{</span></span>
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2183
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<td class="new_line diff-line-num old" data-linenumber="2130" style="width: 35px; color: rgba(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="LC2183" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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2184
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<td class="new_line diff-line-num old" data-linenumber="2130" style="width: 35px; color: rgba(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="LC2184" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">MMs</span><span class="p">;</span></span>
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2185
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<td class="new_line diff-line-num old" data-linenumber="2130" style="width: 35px; color: rgba(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="LC2185" 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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2186
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<td class="new_line diff-line-num old" data-linenumber="2130" style="width: 35px; color: rgba(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="LC2186" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2187
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<td class="new_line diff-line-num old" data-linenumber="2130" style="width: 35px; color: rgba(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="LC2187" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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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2188
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<td class="new_line diff-line-num old" data-linenumber="2130" style="width: 35px; color: rgba(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="LC2188" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">Ms</span><span class="p">;</span></span>
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2189
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<td class="new_line diff-line-num old" data-linenumber="2130" style="width: 35px; color: rgba(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="LC2189" class="line" lang="c"> <span class="p">}</span></span>
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2190
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<td class="new_line diff-line-num old" data-linenumber="2130" style="width: 35px; color: rgba(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="LC2190" class="line" lang="c"> <span class="p">}</span></span>
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2130
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<pre style="margin: 0;">+<span id="LC2130" class="line" lang="c"> </span>
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2131
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<pre style="margin: 0;">+<span id="LC2131" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* evaluate best option */</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2191" style="width: 35px; color: rgba(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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2132
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<pre style="margin: 0;">+<span id="LC2132" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</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;">gaps</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 class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">))</span> <span class="p">{</span></span>
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2133
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<pre style="margin: 0;">+<span id="LC2133" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">);</span></span>
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2191
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2134
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<pre style="margin: 0;"> <span id="LC2134" 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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2192
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<td class="new_line diff-line-num old" data-linenumber="2135" style="width: 35px; color: rgba(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="LC2192" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">MM</span><span class="p">;</span></span>
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2193
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<td class="new_line diff-line-num old" data-linenumber="2135" style="width: 35px; color: rgba(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="LC2193" class="line" lang="c"> <span class="p">}</span></span>
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2194
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<td class="new_line diff-line-num old" data-linenumber="2135" style="width: 35px; color: rgba(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="LC2194" 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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2195
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<td class="new_line diff-line-num old" data-linenumber="2135" style="width: 35px; color: rgba(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="LC2195" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2196
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<td class="new_line diff-line-num old" data-linenumber="2135" style="width: 35px; color: rgba(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="LC2196" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2197
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<td class="new_line diff-line-num old" data-linenumber="2135" style="width: 35px; color: rgba(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="LC2197" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2198
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<pre style="margin: 0;">-<span id="LC2198" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">]</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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2135
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<pre style="margin: 0;">+<span id="LC2135" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</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;">gaps</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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2199
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2136
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<pre style="margin: 0;"> <span id="LC2136" class="line" lang="c"> <span class="p">}</span></span>
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2137
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<pre style="margin: 0;">+<span id="LC2137" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*else {</span></span>
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2138
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<pre style="margin: 0;">+<span id="LC2138" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // unlikely deletion or random k-mer mismatch, </span></span>
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2139
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<pre style="margin: 0;">+<span id="LC2139" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // assume better and go random zero score</span></span>
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2140
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<pre style="margin: 0;">+<span id="LC2140" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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2141
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<pre style="margin: 0;">+<span id="LC2141" 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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2142
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<pre style="margin: 0;">+<span id="LC2142" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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2143
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<pre style="margin: 0;">+<span id="LC2143" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2144
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<pre style="margin: 0;">+<span id="LC2144" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2145
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<pre style="margin: 0;">+<span id="LC2145" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">]</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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2200
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2146
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<pre style="margin: 0;"> <span id="LC2146" class="line" lang="c"> <span class="p">}</span></span>
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2201
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2147
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<pre style="margin: 0;"> <span id="LC2147" class="line" lang="c"> <span class="p">}</span></span>
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2202
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2148
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<pre style="margin: 0;"> <span id="LC2148" class="line" lang="c"> <span class="p">}</span></span>
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2203
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<pre style="margin: 0;">-<span id="LC2203" 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;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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2204
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<pre style="margin: 0;">-<span id="LC2204" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2205
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<pre style="margin: 0;">-<span id="LC2205" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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2206
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<pre style="margin: 0;">-<span id="LC2206" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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2207
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<pre style="margin: 0;">-<span id="LC2207" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2208
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<pre style="margin: 0;">-<span id="LC2208" class="line" lang="c"> <span class="n" style="color: #333;">Score</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2209
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<pre style="margin: 0;">-<span id="LC2209" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2210" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</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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2211
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<pre style="margin: 0;">-<span id="LC2211" class="line" lang="c"> <span class="p">}</span></span>
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2212
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<pre style="margin: 0;">-<span id="LC2212" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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2213
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2149
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<pre style="margin: 0;"> <span id="LC2149" 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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2214
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<td class="new_line diff-line-num old" data-linenumber="2150" style="width: 35px; color: rgba(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="LC2214" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2150
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<pre style="margin: 0;">+<span id="LC2150" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2151
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<pre style="margin: 0;">+<span id="LC2151" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2152
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<pre style="margin: 0;">+<span id="LC2152" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2215
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2153
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<pre style="margin: 0;"> <span id="LC2153" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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2216
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2154
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<pre style="margin: 0;"> <span id="LC2154" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2217
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<pre style="margin: 0;">-<span id="LC2217" class="line" lang="c"> <span class="n" style="color: #333;">Score</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2155
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<pre style="margin: 0;">+<span id="LC2155" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2156
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<pre style="margin: 0;">+<span id="LC2156" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">Ms</span><span class="p">;</span></span>
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2218
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2157
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<pre style="margin: 0;"> <span id="LC2157" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2219
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2158
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<pre style="margin: 0;"> <span id="LC2158" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</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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2220
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2159
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<pre style="margin: 0;"> <span id="LC2159" class="line" lang="c"> <span class="p">}</span></span>
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2221
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2160
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<pre style="margin: 0;"> <span id="LC2160" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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2222
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2161
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<pre style="margin: 0;"> <span id="LC2161" class="line" lang="c"> <span class="p">}</span></span>
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2223
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<pre style="margin: 0;">-<span id="LC2223" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2162
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<pre style="margin: 0;">+<span id="LC2162" class="line" lang="c"> </span>
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2163
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<pre style="margin: 0;">+<span id="LC2163" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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2224
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2164
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<pre style="margin: 0;"> <span id="LC2164" class="line" lang="c"> <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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2225
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<td class="new_line diff-line-num" data-linenumber="2165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2165
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<pre style="margin: 0;"> <span id="LC2165" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2226
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2166
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<pre style="margin: 0;"> <span id="LC2166" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2227
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2167
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<pre style="margin: 0;"> <span id="LC2167" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2228
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2168
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<pre style="margin: 0;"> <span id="LC2168" class="line" lang="c"> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2229
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<td class="new_line diff-line-num old" data-linenumber="2169" style="width: 35px; color: rgba(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="LC2229" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2230
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2169
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<pre style="margin: 0;"> <span id="LC2169" class="line" lang="c"> <span class="p">}</span></span>
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2231
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2170
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<pre style="margin: 0;"> <span id="LC2170" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">hitCounter</span><span class="p">;</span></span>
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2232
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<td class="new_line diff-line-num" data-linenumber="2171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2171
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<pre style="margin: 0;"> <span id="LC2171" 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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2233
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2172
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<pre style="margin: 0;"> <span id="LC2172" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2234
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2173
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<pre style="margin: 0;"> <span id="LC2173" class="line" lang="c"> <span class="p">}</span></span>
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2235
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2174
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<pre style="margin: 0;"> <span id="LC2174" class="line" lang="c"> <span class="p">}</span></span>
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2175
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<pre style="margin: 0;">+<span id="LC2175" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">+=</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;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gap over N's */</span></span>
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2236
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2176
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<pre style="margin: 0;"> <span id="LC2176" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2237
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2177
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<pre style="margin: 0;"> <span id="LC2177" class="line" lang="c"> <span class="p">}</span></span>
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2238
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2178
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<pre style="margin: 0;"> <span id="LC2178" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</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="2294" style="width: 35px; color: rgba(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">@@ -2294,7 +2234,7 @@ int save_kmers_pseuodeSparse(const HashMapKMA *templates, const Penalties *rewar</td>
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2294
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2234
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<pre style="margin: 0;"> <span id="LC2234" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</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;">bestScore</span><span class="p">;</span></span>
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2295
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2235
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<pre style="margin: 0;"> <span id="LC2235" class="line" lang="c"> </span>
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2296
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2236
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<pre style="margin: 0;"> <span id="LC2236" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2297
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<pre style="margin: 0;">-<span id="LC2297" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&&</span></span> <span class="n" style="color: #333;">bestScore</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;">end</span><span class="p">)</span> <span class="p">{</span></span>
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2237
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<pre style="margin: 0;">+<span id="LC2237" 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">kmersize</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;">bestScore</span> <span class="o" style="font-weight: 600;"><span class="idiff right">||</span></span> <span class="n" style="color: #333;">bestScore</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;">end</span><span class="p">)</span> <span class="p">{</span></span>
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2298
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2238
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<pre style="margin: 0;"> <span id="LC2238" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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2299
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2239
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<pre style="margin: 0;"> <span id="LC2239" 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;">deConPrintPtr</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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2300
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2240
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<pre style="margin: 0;"> <span id="LC2240" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2306" style="width: 35px; color: rgba(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="2246" style="width: 35px; color: rgba(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">@@ -2306,7 +2246,7 @@ int save_kmers_pseuodeSparse(const HashMapKMA *templates, const Penalties *rewar</td>
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2306
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2246
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<pre style="margin: 0;"> <span id="LC2246" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">save_kmers</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">extendScore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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2307
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2247
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<pre style="margin: 0;"> <span id="LC2247" class="line" lang="c"> </span>
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2308
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2248
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<pre style="margin: 0;"> <span id="LC2248" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">HIT</span><span class="p">,</span> <span class="n" style="color: #333;">gaps</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">Us</span><span class="p">,</span> <span class="n" style="color: #333;">W1s</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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2309
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<td class="new_line diff-line-num old" data-linenumber="2249" style="width: 35px; color: rgba(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="LC2309" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">hitCounter</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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2249
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<pre style="margin: 0;">+<span id="LC2249" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">hitCounter</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mm</span></span><span class="p">;</span></span>
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2310
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2250
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<pre style="margin: 0;"> <span id="LC2250" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">SU</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">;</span></span>
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2311
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2251
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<pre style="margin: 0;"> <span id="LC2251" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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2312
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2252
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<pre style="margin: 0;"> <span id="LC2252" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">include</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2377" style="width: 35px; color: rgba(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="2317" style="width: 35px; color: rgba(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">@@ -2377,156 +2317,132 @@ int save_kmers(const HashMapKMA *templates, const Penalties *rewards, int *bestT</td>
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2377
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2317
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<pre style="margin: 0;"> <span id="LC2317" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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2378
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2318
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<pre style="margin: 0;"> <span id="LC2318" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashMap_get</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">getKmer</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;">j</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">))))</span> <span class="p">{</span></span>
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2379
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2319
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<pre style="margin: 0;"> <span id="LC2319" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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2380
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<pre style="margin: 0;">-<span id="LC2380" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2320
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<pre style="margin: 0;">+<span id="LC2320" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2321
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<pre style="margin: 0;">+<span id="LC2321" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps == 0 -> Match</span></span>
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2322
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<pre style="margin: 0;">+<span id="LC2322" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps == kmersize -> 1 MM</span></span>
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2323
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<pre style="margin: 0;">+<span id="LC2323" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> kmersize < gaps -> several mismatches or indel(s)</span></span>
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2324
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<pre style="margin: 0;">+<span id="LC2324" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps < kmersize -> deletion</span></span>
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2325
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<pre style="margin: 0;">+<span id="LC2325" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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2326
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<pre style="margin: 0;">+<span id="LC2326" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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 class="p">{</span></span>
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2327
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<pre style="margin: 0;">+<span id="LC2327" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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2328
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<pre style="margin: 0;">+<span id="LC2328" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2329
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<pre style="margin: 0;">+<span id="LC2329" 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;">gaps</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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2330
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<pre style="margin: 0;">+<span id="LC2330" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* snp */</span></span>
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2381
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2331
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<pre style="margin: 0;"> <span id="LC2331" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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2382
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<pre style="margin: 0;">-<span id="LC2382" class="line" lang="c"> <span class="n" style="color: #333;">gaps</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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2383
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<pre style="margin: 0;">-<span id="LC2383" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2384
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<pre style="margin: 0;">-<span id="LC2384" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* go for best scenario */</span></span>
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2385
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<pre style="margin: 0;">-<span id="LC2385" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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2386
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<pre style="margin: 0;">-<span id="LC2386" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2387
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<pre style="margin: 0;">-<span id="LC2387" 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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2388
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<pre style="margin: 0;">-<span id="LC2388" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2389
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<pre style="margin: 0;">-<span id="LC2389" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">MM</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;">gaps</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2390
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<pre style="margin: 0;">-<span id="LC2390" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2391" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2392" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC2393" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2332" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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2333
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<pre style="margin: 0;">+<span id="LC2333" 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;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2334
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<pre style="margin: 0;">+<span id="LC2334" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mismatch or insersion */</span></span>
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2335
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<pre style="margin: 0;">+<span id="LC2335" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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2336
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<pre style="margin: 0;">+<span id="LC2336" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* adjust for consecutive k-mer mismatches */</span></span>
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2337
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<pre style="margin: 0;">+<span id="LC2337" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2338
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<pre style="margin: 0;">+<span id="LC2338" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2339
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<pre style="margin: 0;">+<span id="LC2339" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2340
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<pre style="margin: 0;"> <span id="LC2340" 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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2395
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<pre style="margin: 0;">-<span id="LC2395" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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2341
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<pre style="margin: 0;">+<span id="LC2341" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2342
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<pre style="margin: 0;">+<span id="LC2342" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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2343
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<pre style="margin: 0;">+<span id="LC2343" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</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;">mm</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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2344
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<pre style="margin: 0;">+<span id="LC2344" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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2396
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2345
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<pre style="margin: 0;"> <span id="LC2345" class="line" lang="c"> <span class="p">}</span></span>
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2397
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<pre style="margin: 0;">-<span id="LC2397" 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;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2398
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<pre style="margin: 0;">-<span id="LC2398" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2399
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<pre style="margin: 0;">-<span id="LC2399" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2400" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2401" 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="LC2402" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2403
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<pre style="margin: 0;">-<span id="LC2403" class="line" lang="c"> <span class="p">}</span></span>
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2346
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<pre style="margin: 0;">+<span id="LC2346" class="line" lang="c"> </span>
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2347
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<pre style="margin: 0;">+<span id="LC2347" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* evaluate best option */</span></span>
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2348
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<pre style="margin: 0;">+<span id="LC2348" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</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;">gaps</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 class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">))</span> <span class="p">{</span></span>
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2349
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<pre style="margin: 0;">+<span id="LC2349" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mm</span><span class="p">;</span></span>
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2350
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<pre style="margin: 0;">+<span id="LC2350" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">m</span><span class="p">;</span></span>
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2351
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<pre style="margin: 0;">+<span id="LC2351" 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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2352
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<pre style="margin: 0;">+<span id="LC2352" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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2353
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<pre style="margin: 0;">+<span id="LC2353" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</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;">1</span><span class="p">);</span></span>
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2354
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<pre style="margin: 0;">+<span id="LC2354" class="line" lang="c"> <span class="p">}</span></span>
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2355
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<pre style="margin: 0;">+<span id="LC2355" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*else {</span></span>
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2356
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<pre style="margin: 0;">+<span id="LC2356" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // unlikely deletion or random k-mer mismatch, </span></span>
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2357
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<pre style="margin: 0;">+<span id="LC2357" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // assume better and go random zero score</span></span>
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2358
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<pre style="margin: 0;">+<span id="LC2358" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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2359
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<pre style="margin: 0;">+<span id="LC2359" class="line" lang="c"> </span>
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2404
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2360
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<pre style="margin: 0;"> <span id="LC2360" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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2405
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2361
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<pre style="margin: 0;"> <span id="LC2361" class="line" lang="c"> <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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2406
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2362
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<pre style="margin: 0;"> <span id="LC2362" 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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2407
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2363
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<pre style="margin: 0;"> <span id="LC2363" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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2408
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<pre style="margin: 0;">-<span id="LC2408" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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2409
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<pre style="margin: 0;">-<span id="LC2409" class="line" lang="c"> <span class="n" style="color: #333;">HIT</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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2410
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<pre style="margin: 0;">-<span id="LC2410" 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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2411
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<pre style="margin: 0;">-<span id="LC2411" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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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2412
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<pre style="margin: 0;">-<span id="LC2412" class="line" lang="c"> <span class="p">}</span></span>
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2413
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2364
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<pre style="margin: 0;"> <span id="LC2364" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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2414
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<pre style="margin: 0;">-<span id="LC2414" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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2415
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<pre style="margin: 0;">-<span id="LC2415" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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2416
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<pre style="margin: 0;">-<span id="LC2416" class="line" lang="c"> <span class="n" style="color: #333;">l</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;">values_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2417
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<pre style="margin: 0;">-<span id="LC2417" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2418
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<pre style="margin: 0;">-<span id="LC2418" class="line" lang="c"> <span class="n" style="color: #333;">Score</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2419" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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2420
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<pre style="margin: 0;">-<span id="LC2420" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC2421" class="line" lang="c"> </span>
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2422
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<pre style="margin: 0;">-<span id="LC2422" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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2423
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<pre style="margin: 0;">-<span id="LC2423" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</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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2424
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<pre style="margin: 0;">-<span id="LC2424" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><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="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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2426
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<pre style="margin: 0;">-<span id="LC2426" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2427
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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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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2429
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2429" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">M</span><span class="p">;</span></span>
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2430
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2430" 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="old_line diff-line-num old" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2431
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2431" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</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="old_line diff-line-num old" data-linenumber="2432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2432
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2432" class="line" lang="c"> <span class="n" style="color: #333;">Score</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="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</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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2433
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2433" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2434
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2434" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Score</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2435
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2435" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2436
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2436" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">extendScore</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;">j</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2437
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2437" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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2438
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2438" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">MMs</span><span class="p">;</span></span>
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2439
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2439" 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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2440
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2440" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2441
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2441" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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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2442
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2442" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">Ms</span><span class="p">;</span></span>
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2443
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<pre style="margin: 0;">-<span id="LC2443" class="line" lang="c"> <span class="p">}</span></span>
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2444
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<pre style="margin: 0;">-<span id="LC2444" class="line" lang="c"> <span class="p">}</span></span>
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2445
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2445" 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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2446
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2446" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">MM</span><span class="p">;</span></span>
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2447
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<pre style="margin: 0;">-<span id="LC2447" class="line" lang="c"> <span class="p">}</span></span>
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2448
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2448" 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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2449
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<pre style="margin: 0;">-<span id="LC2449" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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2450
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<pre style="margin: 0;">-<span id="LC2450" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2451
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2451" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2452
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2452" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">]</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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2453
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2453" class="line" lang="c"> <span class="p">}</span></span>
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2454
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2454" class="line" lang="c"> <span class="p">}</span></span>
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2455
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2455" class="line" lang="c"> <span class="p">}</span></span>
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2456
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2456" 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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2457
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2457" class="line" lang="c"> <span class="n" style="color: #333;">l</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;">last</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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2458
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<pre style="margin: 0;">-<span id="LC2458" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2459
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2459" class="line" lang="c"> <span class="n" style="color: #333;">Score</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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2460
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<pre style="margin: 0;">-<span id="LC2460" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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2461
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<pre style="margin: 0;">-<span id="LC2461" class="line" lang="c"> <span class="p">}</span></span>
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2462
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<pre style="margin: 0;">-<span id="LC2462" class="line" lang="c"> </span>
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<td class="old_line diff-line-num old" data-linenumber="2463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2463
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2463" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2464
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2464" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</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="old_line diff-line-num old" data-linenumber="2465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2465
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2465" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2466
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<pre style="margin: 0;">-<span id="LC2466" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2467
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2467" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])])</span> <span class="p">{</span></span>
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2468
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2468" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2469
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<td class="new_line diff-line-num old" data-linenumber="2365" style="width: 35px; color: rgba(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="LC2469" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">M</span><span class="p">;</span></span>
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2365
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<pre style="margin: 0;">+<span id="LC2365" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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2366
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<pre style="margin: 0;">+<span id="LC2366" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</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;">values_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</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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2367
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<pre style="margin: 0;">+<span id="LC2367" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2368
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<pre style="margin: 0;">+<span id="LC2368" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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2369
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<pre style="margin: 0;">+<span id="LC2369" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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2370
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<pre style="margin: 0;">+<span id="LC2370" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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2371
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<pre style="margin: 0;">+<span id="LC2371" class="line" lang="c"> <span class="p">}</span></span>
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2372
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<pre style="margin: 0;">+<span id="LC2372" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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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2373
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<pre style="margin: 0;">+<span id="LC2373" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2374
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<pre style="margin: 0;">+<span id="LC2374" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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2375
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<pre style="margin: 0;">+<span id="LC2375" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2376
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<pre style="margin: 0;">+<span id="LC2376" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2377
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<pre style="margin: 0;">+<span id="LC2377" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2378
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<pre style="margin: 0;">+<span id="LC2378" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2379
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<pre style="margin: 0;">+<span id="LC2379" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2380
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<pre style="margin: 0;">+<span id="LC2380" 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="p">[</span><span class="n" style="color: #333;">template</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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2381
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<pre style="margin: 0;">+<span id="LC2381" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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2382
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<pre style="margin: 0;">+<span id="LC2382" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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 class="p">{</span></span>
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2383
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<pre style="margin: 0;">+<span id="LC2383" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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2384
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<pre style="margin: 0;">+<span id="LC2384" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">M</span><span class="p">;</span></span>
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2385
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<pre style="margin: 0;">+<span id="LC2385" 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;">gaps</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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2386
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<pre style="margin: 0;">+<span id="LC2386" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* snp */</span></span>
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2387
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<pre style="margin: 0;">+<span id="LC2387" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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2388
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<pre style="margin: 0;">+<span id="LC2388" 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;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2389
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<pre style="margin: 0;">+<span id="LC2389" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mismatch or insersion */</span></span>
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2390
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<pre style="margin: 0;">+<span id="LC2390" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* adjust for consecutive k-mer mismatches */</span></span>
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2391
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<pre style="margin: 0;">+<span id="LC2391" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2392
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<pre style="margin: 0;">+<span id="LC2392" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2393
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<pre style="margin: 0;">+<span id="LC2393" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2470
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2394
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<pre style="margin: 0;"> <span id="LC2394" 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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2471
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<td class="new_line diff-line-num old" data-linenumber="2395" style="width: 35px; color: rgba(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="LC2471" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</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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2472
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<pre style="margin: 0;">-<span id="LC2472" class="line" lang="c"> <span class="n" style="color: #333;">Score</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="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</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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2395
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<pre style="margin: 0;">+<span id="LC2395" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2396
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<pre style="margin: 0;">+<span id="LC2396" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2397
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<pre style="margin: 0;">+<span id="LC2397" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</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;">mm</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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2398
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<pre style="margin: 0;">+<span id="LC2398" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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2473
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2399
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<pre style="margin: 0;"> <span id="LC2399" class="line" lang="c"> <span class="p">}</span></span>
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2474
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<pre style="margin: 0;">-<span id="LC2474" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Score</span><span class="p">[</span><span class="n" style="color: #333;">template</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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2475
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<pre style="margin: 0;">-<span id="LC2475" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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2476
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<pre style="margin: 0;">-<span id="LC2476" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">extendScore</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;">j</span><span class="p">))</span> <span class="p">{</span></span>
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2477
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<pre style="margin: 0;">-<span id="LC2477" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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2478
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<td class="new_line diff-line-num old" data-linenumber="2400" style="width: 35px; color: rgba(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="LC2478" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">MMs</span><span class="p">;</span></span>
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2479
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<td class="new_line diff-line-num old" data-linenumber="2400" style="width: 35px; color: rgba(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="LC2479" 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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2480
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<td class="new_line diff-line-num old" data-linenumber="2400" style="width: 35px; color: rgba(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="LC2480" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2481
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<td class="new_line diff-line-num old" data-linenumber="2400" style="width: 35px; color: rgba(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="LC2481" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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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2482
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<td class="new_line diff-line-num old" data-linenumber="2400" style="width: 35px; color: rgba(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="LC2482" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">Ms</span><span class="p">;</span></span>
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2483
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<pre style="margin: 0;">-<span id="LC2483" class="line" lang="c"> <span class="p">}</span></span>
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2484
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<pre style="margin: 0;">-<span id="LC2484" class="line" lang="c"> <span class="p">}</span></span>
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2400
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<pre style="margin: 0;">+<span id="LC2400" class="line" lang="c"> </span>
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2401
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<pre style="margin: 0;">+<span id="LC2401" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* evaluate best option */</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2485" style="width: 35px; color: rgba(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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2402
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<pre style="margin: 0;">+<span id="LC2402" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</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;">gaps</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 class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">))</span> <span class="p">{</span></span>
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2403
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<pre style="margin: 0;">+<span id="LC2403" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">);</span></span>
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2485
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2404
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<pre style="margin: 0;"> <span id="LC2404" 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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2486
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<td class="new_line diff-line-num old" data-linenumber="2405" style="width: 35px; color: rgba(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="LC2486" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">MM</span><span class="p">;</span></span>
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2487
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<pre style="margin: 0;">-<span id="LC2487" class="line" lang="c"> <span class="p">}</span></span>
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2488
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<pre style="margin: 0;">-<span id="LC2488" 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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2489
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<pre style="margin: 0;">-<span id="LC2489" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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2490
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<td class="new_line diff-line-num old" data-linenumber="2405" style="width: 35px; color: rgba(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="LC2490" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2491
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<td class="new_line diff-line-num old" data-linenumber="2405" style="width: 35px; color: rgba(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="LC2491" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2492
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<pre style="margin: 0;">-<span id="LC2492" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">]</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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2405
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<pre style="margin: 0;">+<span id="LC2405" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</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;">gaps</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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2493
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2406
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<pre style="margin: 0;"> <span id="LC2406" class="line" lang="c"> <span class="p">}</span></span>
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2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*else {</span></span>
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2408
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<pre style="margin: 0;">+<span id="LC2408" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // unlikely deletion or random k-mer mismatch, </span></span>
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2409
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<pre style="margin: 0;">+<span id="LC2409" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // assume better and go random zero score</span></span>
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2410
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<pre style="margin: 0;">+<span id="LC2410" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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2411
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<pre style="margin: 0;">+<span id="LC2411" 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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2412
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<pre style="margin: 0;">+<span id="LC2412" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">score</span><span class="p">;</span></span>
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2413
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<pre style="margin: 0;">+<span id="LC2413" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2414
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<pre style="margin: 0;">+<span id="LC2414" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2415
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<pre style="margin: 0;">+<span id="LC2415" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">]</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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2494
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2416
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<pre style="margin: 0;"> <span id="LC2416" class="line" lang="c"> <span class="p">}</span></span>
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2495
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2417
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<pre style="margin: 0;"> <span id="LC2417" class="line" lang="c"> <span class="p">}</span></span>
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2496
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2418
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<pre style="margin: 0;"> <span id="LC2418" class="line" lang="c"> <span class="p">}</span></span>
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2497
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<pre style="margin: 0;">-<span id="LC2497" 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;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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2498
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<pre style="margin: 0;">-<span id="LC2498" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2499
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<pre style="margin: 0;">-<span id="LC2499" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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2500
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<pre style="margin: 0;">-<span id="LC2500" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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2501
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<pre style="margin: 0;">-<span id="LC2501" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2502
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<pre style="margin: 0;">-<span id="LC2502" class="line" lang="c"> <span class="n" style="color: #333;">Score</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2503
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<pre style="margin: 0;">-<span id="LC2503" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2504" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</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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2505
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<pre style="margin: 0;">-<span id="LC2505" class="line" lang="c"> <span class="p">}</span></span>
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2506
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<pre style="margin: 0;">-<span id="LC2506" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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2507
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2419
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<pre style="margin: 0;"> <span id="LC2419" 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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2508
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<td class="new_line diff-line-num old" data-linenumber="2420" style="width: 35px; color: rgba(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="LC2508" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2420
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<pre style="margin: 0;">+<span id="LC2420" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2421
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<pre style="margin: 0;">+<span id="LC2421" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2422
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<pre style="margin: 0;">+<span id="LC2422" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2509
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2423
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<pre style="margin: 0;"> <span id="LC2423" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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2510
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2424
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<pre style="margin: 0;"> <span id="LC2424" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2511
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<pre style="margin: 0;">-<span id="LC2511" class="line" lang="c"> <span class="n" style="color: #333;">Score</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2425
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<pre style="margin: 0;">+<span id="LC2425" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2426
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<pre style="margin: 0;">+<span id="LC2426" class="line" lang="c"> <span class="n" style="color: #333;">Score</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;">Ms</span><span class="p">;</span></span>
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2512
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2427
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<pre style="margin: 0;"> <span id="LC2427" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2513
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2428
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<pre style="margin: 0;"> <span id="LC2428" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</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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2514
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2429
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<pre style="margin: 0;"> <span id="LC2429" class="line" lang="c"> <span class="p">}</span></span>
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2515
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2430
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<pre style="margin: 0;"> <span id="LC2430" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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2516
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2431
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<pre style="margin: 0;"> <span id="LC2431" class="line" lang="c"> <span class="p">}</span></span>
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2517
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<pre style="margin: 0;">-<span id="LC2517" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2432
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<pre style="margin: 0;">+<span id="LC2432" class="line" lang="c"> </span>
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2433
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<pre style="margin: 0;">+<span id="LC2433" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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2518
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<td class="new_line diff-line-num" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2434
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<pre style="margin: 0;"> <span id="LC2434" class="line" lang="c"> <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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2519
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2435
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<pre style="margin: 0;"> <span id="LC2435" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2520
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2436
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<pre style="margin: 0;"> <span id="LC2436" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2521
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<td class="new_line diff-line-num" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2437
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<pre style="margin: 0;"> <span id="LC2437" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2522
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2438
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<pre style="margin: 0;"> <span id="LC2438" class="line" lang="c"> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2523
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<td class="new_line diff-line-num old" data-linenumber="2439" style="width: 35px; color: rgba(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="LC2523" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2524
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2439
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<pre style="margin: 0;"> <span id="LC2439" class="line" lang="c"> <span class="p">}</span></span>
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2525
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2440
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<pre style="margin: 0;"> <span id="LC2440" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">hitCounter</span><span class="p">;</span></span>
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2526
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2441
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<pre style="margin: 0;"> <span id="LC2441" 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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2527
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2442
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<pre style="margin: 0;"> <span id="LC2442" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2528
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2443
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<pre style="margin: 0;"> <span id="LC2443" class="line" lang="c"> <span class="p">}</span></span>
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2529
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2444
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<pre style="margin: 0;"> <span id="LC2444" class="line" lang="c"> <span class="p">}</span></span>
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2445
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<pre style="margin: 0;">+<span id="LC2445" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">+=</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;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gap over N's */</span></span>
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2530
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2446
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<pre style="margin: 0;"> <span id="LC2446" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2531
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2447
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<pre style="margin: 0;"> <span id="LC2447" class="line" lang="c"> <span class="p">}</span></span>
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2532
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2448
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<pre style="margin: 0;"> <span id="LC2448" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</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="2620" style="width: 35px; color: rgba(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">@@ -2620,156 +2536,132 @@ int save_kmers(const HashMapKMA *templates, const Penalties *rewards, int *bestT</td>
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2620
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2536
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<pre style="margin: 0;"> <span id="LC2536" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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2621
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2537
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<pre style="margin: 0;"> <span id="LC2537" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashMap_get</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">getKmer</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">))))</span> <span class="p">{</span></span>
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2622
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2538
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<pre style="margin: 0;"> <span id="LC2538" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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2623
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<pre style="margin: 0;">-<span id="LC2623" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2539
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<pre style="margin: 0;">+<span id="LC2539" 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="LC2540" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps == 0 -> Match</span></span>
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2541
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<pre style="margin: 0;">+<span id="LC2541" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps == kmersize -> 1 MM</span></span>
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2542
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<pre style="margin: 0;">+<span id="LC2542" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> kmersize < gaps -> several mismatches or indel(s)</span></span>
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2543
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<pre style="margin: 0;">+<span id="LC2543" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> gaps < kmersize -> deletion</span></span>
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2544
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<pre style="margin: 0;">+<span id="LC2544" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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2545
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<pre style="margin: 0;">+<span id="LC2545" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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 class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2546
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<pre style="margin: 0;">+<span id="LC2546" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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2547
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<pre style="margin: 0;">+<span id="LC2547" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2548
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<pre style="margin: 0;">+<span id="LC2548" 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;">gaps</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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2549
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<pre style="margin: 0;">+<span id="LC2549" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* snp */</span></span>
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2624
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2550
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<pre style="margin: 0;"> <span id="LC2550" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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2625
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<pre style="margin: 0;">-<span id="LC2625" class="line" lang="c"> <span class="n" style="color: #333;">gaps</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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2626
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<pre style="margin: 0;">-<span id="LC2626" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2627
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<pre style="margin: 0;">-<span id="LC2627" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* go for best scenario */</span></span>
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2628
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<pre style="margin: 0;">-<span id="LC2628" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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2629
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<pre style="margin: 0;">-<span id="LC2629" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2630
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<pre style="margin: 0;">-<span id="LC2630" 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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2631
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<pre style="margin: 0;">-<span id="LC2631" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2632
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<pre style="margin: 0;">-<span id="LC2632" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">MM</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;">gaps</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2633
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<pre style="margin: 0;">-<span id="LC2633" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2634
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<pre style="margin: 0;">-<span id="LC2634" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2635
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<pre style="margin: 0;">-<span id="LC2635" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC2636" class="line" lang="c"> <span class="p">}</span></span>
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2551
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<pre style="margin: 0;">+<span id="LC2551" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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2552
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<pre style="margin: 0;">+<span id="LC2552" 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;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2553
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<pre style="margin: 0;">+<span id="LC2553" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mismatch or insersion */</span></span>
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2554
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<pre style="margin: 0;">+<span id="LC2554" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>
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2555
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<pre style="margin: 0;">+<span id="LC2555" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* adjust for consecutive k-mer mismatches */</span></span>
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2556
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<pre style="margin: 0;">+<span id="LC2556" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2557
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<pre style="margin: 0;">+<span id="LC2557" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2558
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<pre style="margin: 0;">+<span id="LC2558" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2637
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2559
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<pre style="margin: 0;"> <span id="LC2559" 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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2638
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<pre style="margin: 0;">-<span id="LC2638" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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2560
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<pre style="margin: 0;">+<span id="LC2560" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2561
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<pre style="margin: 0;">+<span id="LC2561" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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2562
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<pre style="margin: 0;">+<span id="LC2562" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</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;">mm</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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2563
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<pre style="margin: 0;">+<span id="LC2563" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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2639
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2564
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<pre style="margin: 0;"> <span id="LC2564" class="line" lang="c"> <span class="p">}</span></span>
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2640
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<pre style="margin: 0;">-<span id="LC2640" 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;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2641
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<pre style="margin: 0;">-<span id="LC2641" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2642
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<pre style="margin: 0;">-<span id="LC2642" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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2643
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<pre style="margin: 0;">-<span id="LC2643" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2644
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<pre style="margin: 0;">-<span id="LC2644" 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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2645
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<pre style="margin: 0;">-<span id="LC2645" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2646
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<pre style="margin: 0;">-<span id="LC2646" class="line" lang="c"> <span class="p">}</span></span>
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2565
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<pre style="margin: 0;">+<span id="LC2565" class="line" lang="c"> </span>
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2566
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<pre style="margin: 0;">+<span id="LC2566" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* evaluate best option */</span></span>
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2567
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<pre style="margin: 0;">+<span id="LC2567" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</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;">gaps</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 class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">))</span> <span class="p">{</span></span>
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2568
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<pre style="margin: 0;">+<span id="LC2568" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mm</span><span class="p">;</span></span>
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2569
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<pre style="margin: 0;">+<span id="LC2569" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">m</span><span class="p">;</span></span>
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2570
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<pre style="margin: 0;">+<span id="LC2570" 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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2571
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<pre style="margin: 0;">+<span id="LC2571" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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2572
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<pre style="margin: 0;">+<span id="LC2572" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</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;">1</span><span class="p">);</span></span>
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2573
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<pre style="margin: 0;">+<span id="LC2573" class="line" lang="c"> <span class="p">}</span></span>
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2574
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<pre style="margin: 0;">+<span id="LC2574" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*else {</span></span>
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2575
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<pre style="margin: 0;">+<span id="LC2575" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // unlikely deletion or random k-mer mismatch, </span></span>
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2576
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<pre style="margin: 0;">+<span id="LC2576" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // assume better and go random zero score</span></span>
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2577
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<pre style="margin: 0;">+<span id="LC2577" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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2578
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<pre style="margin: 0;">+<span id="LC2578" class="line" lang="c"> </span>
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2647
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2579
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<pre style="margin: 0;"> <span id="LC2579" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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2648
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2580
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<pre style="margin: 0;"> <span id="LC2580" class="line" lang="c"> <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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2649
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2581
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<pre style="margin: 0;"> <span id="LC2581" 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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2650
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2582
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<pre style="margin: 0;"> <span id="LC2582" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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2651
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<pre style="margin: 0;">-<span id="LC2651" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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2652
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<pre style="margin: 0;">-<span id="LC2652" class="line" lang="c"> <span class="n" style="color: #333;">HIT</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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2653
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<pre style="margin: 0;">-<span id="LC2653" 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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2654
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<td class="new_line diff-line-num old" data-linenumber="2583" style="width: 35px; color: rgba(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="LC2654" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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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2655
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<td class="new_line diff-line-num old" data-linenumber="2583" style="width: 35px; color: rgba(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="LC2655" class="line" lang="c"> <span class="p">}</span></span>
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2656
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2583
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<pre style="margin: 0;"> <span id="LC2583" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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2657
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2657" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2658
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2658" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2659
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2659" class="line" lang="c"> <span class="n" style="color: #333;">l</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;">values_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2660
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2660" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2661
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2661" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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2662
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2662" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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2663
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2663" class="line" lang="c"> <span class="p">}</span></span>
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2664
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2664" class="line" lang="c"> </span>
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2665
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2665" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2666
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2666" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</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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2667
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2667" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2668
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2668" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2669
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2669" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2670
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2670" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])])</span> <span class="p">{</span></span>
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2671
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2671" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2672
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2672" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">M</span><span class="p">;</span></span>
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2673
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2673" 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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2674
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2674" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</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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2675
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2675" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</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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2676
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2676" class="line" lang="c"> <span class="p">}</span></span>
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2677
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2677" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Score_r</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2678
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2678" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">score</span><span class="p">;</span></span>
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2679
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2679" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">extendScore</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;">j</span><span class="p">))</span> <span class="p">{</span></span>
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2680
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2680" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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2681
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2681" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">MMs</span><span class="p">;</span></span>
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2682
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2682" 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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2683
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2683" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2684
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2684" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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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2685
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2685" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">Ms</span><span class="p">;</span></span>
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2686
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2686" class="line" lang="c"> <span class="p">}</span></span>
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2687
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2687" class="line" lang="c"> <span class="p">}</span></span>
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2688
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2688" 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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2689
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2689" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">MM</span><span class="p">;</span></span>
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2690
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2690" class="line" lang="c"> <span class="p">}</span></span>
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2691
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2691" 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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2692
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2692" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">score</span><span class="p">;</span></span>
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2693
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2693" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2694
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2694" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2695
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2695" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">]</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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2696
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2696" class="line" lang="c"> <span class="p">}</span></span>
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2697
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2697" class="line" lang="c"> <span class="p">}</span></span>
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2698
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2698" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2699
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2699" 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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2700
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2700" class="line" lang="c"> <span class="n" style="color: #333;">l</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;">last</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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2701
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2701" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2702
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2702" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2703
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2703" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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2704
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2704" class="line" lang="c"> <span class="p">}</span></span>
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2705
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2705" class="line" lang="c"> </span>
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2706
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2706" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2707
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2707" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</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="old_line diff-line-num old" data-linenumber="2708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2708
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2708" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2709
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2709" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2710
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2710" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])])</span> <span class="p">{</span></span>
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2711
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<pre style="margin: 0;">-<span id="LC2711" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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2712
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<td class="new_line diff-line-num old" data-linenumber="2584" style="width: 35px; color: rgba(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="LC2712" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">M</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2584
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<pre style="margin: 0;">+<span id="LC2584" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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2585
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<pre style="margin: 0;">+<span id="LC2585" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</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;">values_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last</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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2586
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<pre style="margin: 0;">+<span id="LC2586" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2587
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<pre style="margin: 0;">+<span id="LC2587" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">last</span><span class="p">;</span></span>
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2588
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<pre style="margin: 0;">+<span id="LC2588" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">score</span><span class="p">;</span></span>
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2589
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<pre style="margin: 0;">+<span id="LC2589" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</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;">HIT</span><span class="p">;</span></span>
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2590
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<pre style="margin: 0;">+<span id="LC2590" class="line" lang="c"> <span class="p">}</span></span>
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2591
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<pre style="margin: 0;">+<span id="LC2591" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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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2592
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<pre style="margin: 0;">+<span id="LC2592" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2593
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<pre style="margin: 0;">+<span id="LC2593" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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2594
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<pre style="margin: 0;">+<span id="LC2594" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2595
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<pre style="margin: 0;">+<span id="LC2595" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2596
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<pre style="margin: 0;">+<span id="LC2596" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2597
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<pre style="margin: 0;">+<span id="LC2597" 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;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2598
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<pre style="margin: 0;">+<span id="LC2598" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2599
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<pre style="margin: 0;">+<span id="LC2599" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Score_r</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2600
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<pre style="margin: 0;">+<span id="LC2600" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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2601
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<pre style="margin: 0;">+<span id="LC2601" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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 class="p">{</span></span>
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2602
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<pre style="margin: 0;">+<span id="LC2602" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* match */</span></span>
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2603
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<pre style="margin: 0;">+<span id="LC2603" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">M</span><span class="p">;</span></span>
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2604
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<pre style="margin: 0;">+<span id="LC2604" 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;">gaps</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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2605
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<pre style="margin: 0;">+<span id="LC2605" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* snp */</span></span>
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2606
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<pre style="margin: 0;">+<span id="LC2606" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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2607
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<pre style="margin: 0;">+<span id="LC2607" 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;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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2608
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<pre style="margin: 0;">+<span id="LC2608" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mismatch or insersion */</span></span>
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2609
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<pre style="margin: 0;">+<span id="LC2609" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* adjust for consecutive k-mer mismatches */</span></span>
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2610
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<pre style="margin: 0;">+<span id="LC2610" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2611
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<pre style="margin: 0;">+<span id="LC2611" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2612
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<pre style="margin: 0;">+<span id="LC2612" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2713
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2613
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<pre style="margin: 0;"> <span id="LC2613" 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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2714
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<td class="new_line diff-line-num old" data-linenumber="2614" style="width: 35px; color: rgba(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="LC2714" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</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;">j</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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2715
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<pre style="margin: 0;">-<span id="LC2715" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</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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2614
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<pre style="margin: 0;">+<span id="LC2614" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2615
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<pre style="margin: 0;">+<span id="LC2615" class="line" lang="c"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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2616
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<pre style="margin: 0;">+<span id="LC2616" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</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;">mm</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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2617
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<pre style="margin: 0;">+<span id="LC2617" class="line" lang="c"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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2716
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2618
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<pre style="margin: 0;"> <span id="LC2618" class="line" lang="c"> <span class="p">}</span></span>
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2717
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<td class="new_line diff-line-num old" data-linenumber="2619" style="width: 35px; color: rgba(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="LC2717" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Score_r</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2718
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<pre style="margin: 0;">-<span id="LC2718" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">score</span><span class="p">;</span></span>
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2719
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<pre style="margin: 0;">-<span id="LC2719" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">extendScore</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;">j</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC2720" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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2721
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<pre style="margin: 0;">-<span id="LC2721" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">MMs</span><span class="p">;</span></span>
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2722
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<pre style="margin: 0;">-<span id="LC2722" 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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2723
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<pre style="margin: 0;">-<span id="LC2723" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2724
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<td class="new_line diff-line-num old" data-linenumber="2619" style="width: 35px; color: rgba(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="LC2724" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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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2725
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<td class="new_line diff-line-num old" data-linenumber="2619" style="width: 35px; color: rgba(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="LC2725" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">Ms</span><span class="p">;</span></span>
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2726
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<pre style="margin: 0;">-<span id="LC2726" class="line" lang="c"> <span class="p">}</span></span>
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2727
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<pre style="margin: 0;">-<span id="LC2727" class="line" lang="c"> <span class="p">}</span></span>
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2619
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<pre style="margin: 0;">+<span id="LC2619" class="line" lang="c"> </span>
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2620
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<pre style="margin: 0;">+<span id="LC2620" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* evaluate best option */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2621
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<pre style="margin: 0;">+<span id="LC2621" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</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;">gaps</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 class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">))</span> <span class="p">{</span></span>
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2622
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<pre style="margin: 0;">+<span id="LC2622" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</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;">M</span><span class="p">);</span></span>
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2728
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2623
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<pre style="margin: 0;"> <span id="LC2623" 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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2729
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<pre style="margin: 0;">-<span id="LC2729" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">MM</span><span class="p">;</span></span>
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2730
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<pre style="margin: 0;">-<span id="LC2730" class="line" lang="c"> <span class="p">}</span></span>
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2731
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<td class="new_line diff-line-num old" data-linenumber="2624" style="width: 35px; color: rgba(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="LC2731" 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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2732
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<td class="new_line diff-line-num old" data-linenumber="2624" style="width: 35px; color: rgba(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="LC2732" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">score</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2733
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<td class="new_line diff-line-num old" data-linenumber="2624" style="width: 35px; color: rgba(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="LC2733" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2734
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<td class="new_line diff-line-num old" data-linenumber="2624" style="width: 35px; color: rgba(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="LC2734" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2735
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<pre style="margin: 0;">-<span id="LC2735" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">]</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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2624
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<pre style="margin: 0;">+<span id="LC2624" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">score</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</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;">gaps</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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2736
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2625
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<pre style="margin: 0;"> <span id="LC2625" class="line" lang="c"> <span class="p">}</span></span>
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2626
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<pre style="margin: 0;">+<span id="LC2626" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*else {</span></span>
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2627
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<pre style="margin: 0;">+<span id="LC2627" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // unlikely deletion or random k-mer mismatch, </span></span>
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2628
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<pre style="margin: 0;">+<span id="LC2628" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // assume better and go random zero score</span></span>
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2629
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<pre style="margin: 0;">+<span id="LC2629" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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2630
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<pre style="margin: 0;">+<span id="LC2630" 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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2631
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<pre style="margin: 0;">+<span id="LC2631" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">score</span><span class="p">;</span></span>
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2632
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<pre style="margin: 0;">+<span id="LC2632" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">include</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2633
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<pre style="margin: 0;">+<span id="LC2633" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2634
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<pre style="margin: 0;">+<span id="LC2634" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">]</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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2737
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2635
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<pre style="margin: 0;"> <span id="LC2635" class="line" lang="c"> <span class="p">}</span></span>
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2738
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2636
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<pre style="margin: 0;"> <span id="LC2636" class="line" lang="c"> <span class="p">}</span></span>
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2739
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2637
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<pre style="margin: 0;"> <span id="LC2637" class="line" lang="c"> <span class="p">}</span></span>
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2740
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<pre style="margin: 0;">-<span id="LC2740" 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;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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2741
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<pre style="margin: 0;">-<span id="LC2741" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2742
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<pre style="margin: 0;">-<span id="LC2742" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span><span class="p">;</span></span>
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2743
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<pre style="margin: 0;">-<span id="LC2743" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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2744
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<pre style="margin: 0;">-<span id="LC2744" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2745
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<pre style="margin: 0;">-<span id="LC2745" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2746
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<pre style="margin: 0;">-<span id="LC2746" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2747
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<pre style="margin: 0;">-<span id="LC2747" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</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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2748
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<pre style="margin: 0;">-<span id="LC2748" class="line" lang="c"> <span class="p">}</span></span>
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2749
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<pre style="margin: 0;">-<span id="LC2749" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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2750
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2638
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<pre style="margin: 0;"> <span id="LC2638" 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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2751
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<td class="new_line diff-line-num old" data-linenumber="2639" style="width: 35px; color: rgba(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="LC2751" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2639
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<pre style="margin: 0;">+<span id="LC2639" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2640
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<pre style="margin: 0;">+<span id="LC2640" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2641
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<pre style="margin: 0;">+<span id="LC2641" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2752
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2642
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<pre style="margin: 0;"> <span id="LC2642" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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2753
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2643
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<pre style="margin: 0;"> <span id="LC2643" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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2754
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<pre style="margin: 0;">-<span id="LC2754" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</span><span class="p">[(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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2644
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<pre style="margin: 0;">+<span id="LC2644" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2645
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<pre style="margin: 0;">+<span id="LC2645" class="line" lang="c"> <span class="n" style="color: #333;">Score_r</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;">Ms</span><span class="p">;</span></span>
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2755
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2646
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<pre style="margin: 0;"> <span id="LC2646" class="line" lang="c"> <span class="n" style="color: #333;">include</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2756
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2647
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<pre style="margin: 0;"> <span id="LC2647" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</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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2757
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2648
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<pre style="margin: 0;"> <span id="LC2648" class="line" lang="c"> <span class="p">}</span></span>
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2758
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2649
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<pre style="margin: 0;"> <span id="LC2649" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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2759
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2650
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<pre style="margin: 0;"> <span id="LC2650" class="line" lang="c"> <span class="p">}</span></span>
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2760
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<pre style="margin: 0;">-<span id="LC2760" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2651
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<pre style="margin: 0;">+<span id="LC2651" class="line" lang="c"> </span>
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2652
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<pre style="margin: 0;">+<span id="LC2652" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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2761
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2653
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<pre style="margin: 0;"> <span id="LC2653" class="line" lang="c"> <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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2762
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2654
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<pre style="margin: 0;"> <span id="LC2654" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2763
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2655
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<pre style="margin: 0;"> <span id="LC2655" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2764
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<td class="new_line diff-line-num" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2656
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<pre style="margin: 0;"> <span id="LC2656" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2765
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<td class="new_line diff-line-num" data-linenumber="2657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2657
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<pre style="margin: 0;"> <span id="LC2657" class="line" lang="c"> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2766
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<td class="new_line diff-line-num old" data-linenumber="2658" style="width: 35px; color: rgba(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="LC2766" class="line" lang="c"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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2767
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2658
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<pre style="margin: 0;"> <span id="LC2658" class="line" lang="c"> <span class="p">}</span></span>
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2768
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<td class="new_line diff-line-num" data-linenumber="2659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2659
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<pre style="margin: 0;"> <span id="LC2659" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">hitCounter</span><span class="p">;</span></span>
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2769
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<td class="new_line diff-line-num" data-linenumber="2660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2660
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<pre style="margin: 0;"> <span id="LC2660" 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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2770
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2661
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<pre style="margin: 0;"> <span id="LC2661" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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2771
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2662
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<pre style="margin: 0;"> <span id="LC2662" class="line" lang="c"> <span class="p">}</span></span>
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2772
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2663
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<pre style="margin: 0;"> <span id="LC2663" class="line" lang="c"> <span class="p">}</span></span>
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2664
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<pre style="margin: 0;">+<span id="LC2664" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">+=</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;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gap over N's */</span></span>
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2773
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2665
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<pre style="margin: 0;"> <span id="LC2665" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2774
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2666
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<pre style="margin: 0;"> <span id="LC2666" class="line" lang="c"> <span class="p">}</span></span>
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2775
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2667
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<pre style="margin: 0;"> <span id="LC2667" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</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="2833" style="width: 35px; color: rgba(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="2725" style="width: 35px; color: rgba(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">@@ -2833,7 +2725,8 @@ int save_kmers(const HashMapKMA *templates, const Penalties *rewards, int *bestT</td>
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2833
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2725
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<pre style="margin: 0;"> <span id="LC2725" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2834
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2726
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<pre style="margin: 0;"> <span id="LC2726" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">bestScore_r</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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2835
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2727
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<pre style="margin: 0;"> <span id="LC2727" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</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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2836
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<td class="new_line diff-line-num old" data-linenumber="2728" style="width: 35px; color: rgba(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="LC2836" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">bestScore_r</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bestScore_r</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bestScore_r</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2728" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if((bestScore >= bestScore_r && bestScore * kmersize > (end - bestScore)) || (bestScore < bestScore_r && bestScore_r * kmersize > (end - bestScore_r))) {</span></span>
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2729
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<pre style="margin: 0;">+<span id="LC2729" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">bestScore</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;">bestScore_r</span><span class="p">)</span> <span class="p">{</span></span>
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2837
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2730
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<pre style="margin: 0;"> <span id="LC2730" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">)</span> <span class="p">{</span></span>
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2838
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2731
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<pre style="margin: 0;"> <span id="LC2731" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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2839
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2732
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<pre style="margin: 0;"> <span id="LC2732" 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;">deConPrintPtr</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3105" style="width: 35px; color: rgba(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="2998" style="width: 35px; color: rgba(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">@@ -3105,7 +2998,8 @@ int save_kmers_count(const HashMapKMA *templates, const Penalties *rewards, int</td>
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3105
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2998
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<pre style="margin: 0;"> <span id="LC2998" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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3106
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2999
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<pre style="margin: 0;"> <span id="LC2999" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">bestScore_r</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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3107
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3000
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<pre style="margin: 0;"> <span id="LC3000" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</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="old_line diff-line-num old" data-linenumber="3108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3108
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<pre style="margin: 0;">-<span id="LC3108" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">bestScore_r</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bestScore_r</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bestScore_r</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">)))</span> <span class="p">{</span></span>
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3001
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<pre style="margin: 0;">+<span id="LC3001" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if((bestScore >= bestScore_r && bestScore * kmersize > (end - bestScore)) || (bestScore < bestScore_r && bestScore_r * kmersize > (end - bestScore_r))) {</span></span>
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3002
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<pre style="margin: 0;">+<span id="LC3002" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">bestScore</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;">bestScore_r</span><span class="p">)</span> <span class="p">{</span></span>
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3109
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3003
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<pre style="margin: 0;"> <span id="LC3003" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">)</span> <span class="p">{</span></span>
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3110
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3004
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<pre style="margin: 0;"> <span id="LC3004" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="3111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3111
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3005
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<pre style="margin: 0;"> <span id="LC3005" 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;">deConPrintPtr</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3148" style="width: 35px; color: rgba(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="3042" style="width: 35px; color: rgba(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">@@ -3148,7 +3042,7 @@ int save_kmers_unionPair(const HashMapKMA *templates, const Penalties *rewards,</td>
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3148
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<td class="new_line diff-line-num" data-linenumber="3042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3042
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<pre style="margin: 0;"> <span id="LC3042" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* got hits */</span></span>
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<td class="old_line diff-line-num" data-linenumber="3149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3149
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<td class="new_line diff-line-num" data-linenumber="3043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3043
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<pre style="margin: 0;"> <span id="LC3043" 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;">getF</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">regionTemplates</span><span class="p">);</span></span>
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3150
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3044
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<pre style="margin: 0;"> <span id="LC3044" class="line" lang="c"> </span>
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3151
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<pre style="margin: 0;">-<span id="LC3151" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore</span><span class="p">))</span> <span class="p">{</span></span>
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3045
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<pre style="margin: 0;">+<span id="LC3045" 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">kmersize</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">bestScore</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;">bestScore</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore</span><span class="p">))</span> <span class="p">{</span></span>
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3152
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<pre style="margin: 0;"> <span id="LC3046" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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3153
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3047
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<pre style="margin: 0;"> <span id="LC3047" class="line" lang="c"> <span class="p">}</span></span>
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3154
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3048
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<pre style="margin: 0;"> <span id="LC3048" 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="3176" style="width: 35px; color: rgba(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="3070" style="width: 35px; color: rgba(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">@@ -3176,7 +3070,7 @@ int save_kmers_unionPair(const HashMapKMA *templates, const Penalties *rewards,</td>
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3176
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3070
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<pre style="margin: 0;"> <span id="LC3070" 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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3177
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3071
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<pre style="margin: 0;"> <span id="LC3071" class="line" lang="c"> <span class="n" style="color: #333;">bestScore_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getF</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">regionTemplates</span><span class="p">);</span></span>
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3178
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3072
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<pre style="margin: 0;"> <span id="LC3072" class="line" lang="c"> <span class="p">}</span></span>
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3179
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<pre style="margin: 0;">-<span id="LC3179" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore_r</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">))</span> <span class="p">{</span></span>
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3073
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<pre style="margin: 0;">+<span id="LC3073" 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">kmersize</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">bestScore_r</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;">bestScore_r</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">))</span> <span class="p">{</span></span>
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3074
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<pre style="margin: 0;"> <span id="LC3074" class="line" lang="c"> <span class="n" style="color: #333;">bestScore_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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3181
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<pre style="margin: 0;"> <span id="LC3075" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">regionTemplates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">regionTemplates</span><span class="p">);</span></span>
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3182
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3076
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<pre style="margin: 0;"> <span id="LC3076" 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">@@ -3379,7 +3273,7 @@ int save_kmers_penaltyPair(const HashMapKMA *templates, const Penalties *rewards</td>
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3379
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<pre style="margin: 0;"> <span id="LC3273" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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3380
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<pre style="margin: 0;"> <span id="LC3274" class="line" lang="c"> <span class="n" style="color: #333;">flag_r</span> <span class="o" style="font-weight: 600;">|=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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3381
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<pre style="margin: 0;"> <span id="LC3275" class="line" lang="c"> <span class="n" style="color: #333;">compScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">((</span><span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hitCounter_r</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">));</span></span>
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3382
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<pre style="margin: 0;">-<span id="LC3382" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">compScore</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">compScore</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC3276" 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">kmersize</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">compScore</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="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">compScore</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">compScore</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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3383
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3277
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<pre style="margin: 0;"> <span id="LC3277" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">regionTemplates</span> <span class="o" style="font-weight: 600;">=</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;">regionTemplates</span><span class="p">);</span></span>
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3384
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3278
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<pre style="margin: 0;"> <span id="LC3278" 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;">regionTemplates</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>
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3385
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3279
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<pre style="margin: 0;"> <span id="LC3279" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rev</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3319" style="width: 35px; color: rgba(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">@@ -3425,7 +3319,7 @@ int save_kmers_penaltyPair(const HashMapKMA *templates, const Penalties *rewards</td>
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3425
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3319
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<pre style="margin: 0;"> <span id="LC3319" class="line" lang="c"> <span class="p">}</span></span>
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3426
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<td class="new_line diff-line-num" data-linenumber="3320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3320
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<pre style="margin: 0;"> <span id="LC3320" 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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3427
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3321
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<pre style="margin: 0;"> <span id="LC3321" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">hitCounter</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">);</span></span>
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3428
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<pre style="margin: 0;">-<span id="LC3428" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hitCounter</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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3322
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<pre style="margin: 0;">+<span id="LC3322" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">kmersize</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">hitCounter</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="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hitCounter</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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3429
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3323
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<pre style="margin: 0;"> <span id="LC3323" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">hitCounter</span><span class="p">)</span> <span class="p">{</span></span>
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3430
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3324
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<pre style="margin: 0;"> <span id="LC3324" 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;">regionTemplates</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>
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3431
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3325
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<pre style="margin: 0;"> <span id="LC3325" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rev</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="3445" style="width: 35px; color: rgba(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="3339" style="width: 35px; color: rgba(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">@@ -3445,7 +3339,7 @@ int save_kmers_penaltyPair(const HashMapKMA *templates, const Penalties *rewards</td>
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3445
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3339
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<pre style="margin: 0;"> <span id="LC3339" class="line" lang="c"> <span class="p">}</span></span>
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3446
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3340
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<pre style="margin: 0;"> <span id="LC3340" class="line" lang="c"> <span class="p">}</span></span>
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3447
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3341
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<pre style="margin: 0;"> <span id="LC3341" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">hitCounter_r</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3448
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<pre style="margin: 0;">-<span id="LC3448" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hitCounter_r</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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3342
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<pre style="margin: 0;">+<span id="LC3342" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">kmersize</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">hitCounter_r</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="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hitCounter_r</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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3449
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3343
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<pre style="margin: 0;"> <span id="LC3343" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">hitCounter_r</span><span class="p">)</span> <span class="p">{</span></span>
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3450
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3344
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<pre style="margin: 0;"> <span id="LC3344" 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;">bestTemplates</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>
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3451
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3345
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<pre style="margin: 0;"> <span id="LC3345" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rev</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="3485" style="width: 35px; color: rgba(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="3379" style="width: 35px; color: rgba(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">@@ -3485,7 +3379,7 @@ int save_kmers_penaltyPair(const HashMapKMA *templates, const Penalties *rewards</td>
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3485
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<td class="new_line diff-line-num" data-linenumber="3379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3379
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<pre style="margin: 0;"> <span id="LC3379" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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3486
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<td class="new_line diff-line-num" data-linenumber="3380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3380
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<pre style="margin: 0;"> <span id="LC3380" 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;">0</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>
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<td class="old_line diff-line-num" data-linenumber="3487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3487
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<td class="new_line diff-line-num" data-linenumber="3381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3381
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<pre style="margin: 0;"> <span id="LC3381" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">hitCounter</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3488
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<td class="new_line diff-line-num old" data-linenumber="3382" style="width: 35px; color: rgba(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="LC3488" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3382
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<pre style="margin: 0;">+<span id="LC3382" 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">kmersize</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">hitCounter</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="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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3489
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3383
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<pre style="margin: 0;"> <span id="LC3383" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rev</span><span class="p">)</span> <span class="p">{</span></span>
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3490
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3384
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<pre style="margin: 0;"> <span id="LC3384" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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3491
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3385
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<pre style="margin: 0;"> <span id="LC3385" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3516" style="width: 35px; color: rgba(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="3410" style="width: 35px; color: rgba(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">@@ -3516,7 +3410,7 @@ int save_kmers_penaltyPair(const HashMapKMA *templates, const Penalties *rewards</td>
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3516
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3410
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<pre style="margin: 0;"> <span id="LC3410" class="line" lang="c"> <span class="p">}</span></span>
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3517
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<td class="new_line diff-line-num" data-linenumber="3411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3411
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<pre style="margin: 0;"> <span id="LC3411" 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;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">)</span> <span class="p">{</span></span>
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3518
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3412
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<pre style="margin: 0;"> <span id="LC3412" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">hitCounter_r</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore_r</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3519
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<td class="new_line diff-line-num old" data-linenumber="3413" style="width: 35px; color: rgba(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="LC3519" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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3413
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<pre style="margin: 0;">+<span id="LC3413" 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">kmersize</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">hitCounter_r</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="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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3414
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<pre style="margin: 0;"> <span id="LC3414" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rev</span><span class="p">)</span> <span class="p">{</span></span>
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3521
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3415
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<pre style="margin: 0;"> <span id="LC3415" class="line" lang="c"> <span class="n" style="color: #333;">flag_r</span> <span class="o" style="font-weight: 600;">|=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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3522
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3416
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<pre style="margin: 0;"> <span id="LC3416" class="line" lang="c"> <span class="n" style="color: #333;">flag_r</span> <span class="o" style="font-weight: 600;">|=</span> <span class="mi" style="color: #099;">32</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">@@ -3578,7 +3472,7 @@ int save_kmers_forcePair(const HashMapKMA *templates, const Penalties *rewards,</td>
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3578
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3472
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<pre style="margin: 0;"> <span id="LC3472" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">hitCounter_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_kmers_for_pair_ptr</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">extendScore</span><span class="p">,</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> </span>
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3579
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3473
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<pre style="margin: 0;"> <span id="LC3473" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSecondForce</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">regionTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">regionScores</span><span class="p">)))</span> <span class="p">{</span></span>
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3580
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3474
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<pre style="margin: 0;"> <span id="LC3474" class="line" lang="c"> </span>
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3581
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<pre style="margin: 0;">-<span id="LC3581" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC3475" 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">kmersize</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">bestScore</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="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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3476
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<pre style="margin: 0;"> <span id="LC3476" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">67</span><span class="p">;</span></span>
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3583
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<pre style="margin: 0;"> <span id="LC3477" class="line" lang="c"> <span class="n" style="color: #333;">flag_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">131</span><span class="p">;</span></span>
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3478
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<pre style="margin: 0;"> <span id="LC3478" class="line" lang="c"> </span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#f80652dda49a7117428c0f92935664fc8cd4e2d1"><strong>spltdb.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="379" style="width: 35px; color: rgba(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="379" style="width: 35px; color: rgba(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">@@ -379,10 +379,10 @@ unsigned get_ankers_spltDB(int *infoSize, int *out_Tem, CompDNA *qseq, Qseqs *he</td>
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"> <span class="n" style="color: #333;">cfread</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC380" 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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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* in the case of equally well scoring DBs */</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="n" style="color: #333;">infoSize</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">infoSize</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">s</span>fseek</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="n" style="color: #333;">infoSize</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">infoSize</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="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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383
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out_Tem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infoSize</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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384
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="c"> <span class="n" style="color: #333;">cfread</span><span class="p">(</span><span class="n" style="color: #333;">out_Tem</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out_Tem</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="n" style="color: #333;">infoSize</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">s</span>fseek</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="n" style="color: #333;">infoSize</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="c"> <span class="p">}</span></span>
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="c"> </span>
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get info for next read */</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -430,6 +430,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="c"> <span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">;</span></span>
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431
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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;">NWmat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NWmatrices</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="c"> <span class="n" style="color: #333;">Assemble_thread</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">threads</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">;</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="c"> <span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_index</span><span class="p">;</span></span>
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC435" 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;">outputfilename</span><span class="p">)</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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" No output file specified!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="472" style="width: 35px; color: rgba(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">@@ -471,6 +472,9 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="c"> <span class="p">}</span></span>
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473
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="c"> <span class="n" style="color: #333;">dbBiases</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB_size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC475" 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;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="c"> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">=</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="LC477" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">||</span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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479
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="c"> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span></span>
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480
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<pre style="margin: 0;"> <span id="LC480" 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">@@ -599,7 +603,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* open input streams */</span></span>
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604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="c"> <span class="n" style="color: #333;">file_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">);</span></span>
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601
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">targetNum</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="s" style="color: #d14;">".%d"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="s" style="color: #d14;">".%d"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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607
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<pre style="margin: 0;"> <span id="LC607" 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;">inputfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)))</span> <span class="p">{</span></span>
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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;">usleep</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">);</span></span>
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609
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<pre style="margin: 0;"> <span id="LC609" 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="1405" style="width: 35px; color: rgba(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">@@ -1401,6 +1405,10 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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1401
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1405
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<pre style="margin: 0;"> <span id="LC1405" 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;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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1402
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1406
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<pre style="margin: 0;"> <span id="LC1406" 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;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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1403
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1407
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<pre style="margin: 0;"> <span id="LC1407" 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;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="c"> <span class="n" style="color: #333;">seq_in_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="c"> <span class="n" style="color: #333;">template_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span><span class="p">));</span></span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="c"> <span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span 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="LC1411" class="line" lang="c"> <span class="n" style="color: #333;">hashMapCCI_initialize</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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1404
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<td class="new_line diff-line-num" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1412
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1405
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<td class="new_line diff-line-num" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* allocate matrcies for NW */</span></span>
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<td class="old_line diff-line-num" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1406
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<td class="new_line diff-line-num" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1455" style="width: 35px; color: rgba(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="1463" style="width: 35px; color: rgba(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">@@ -1455,7 +1463,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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1455
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<td class="new_line diff-line-num" data-linenumber="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1463
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<pre style="margin: 0;"> <span id="LC1463" 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;">points</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seedPoint_init</span><span class="p">(</span><span class="n" style="color: #333;">delta</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1456
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<td class="new_line diff-line-num" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1464
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<pre style="margin: 0;"> <span id="LC1464" 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;">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="old_line diff-line-num" data-linenumber="1457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1457
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<td class="new_line diff-line-num" data-linenumber="1465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1465
</td>
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<pre style="margin: 0;"> <span id="LC1465" 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;">spin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sparse</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1458
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<td class="new_line diff-line-num old" data-linenumber="1466" style="width: 35px; color: rgba(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="LC1458" class="line" lang="c"> </span>
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<td class="new_line diff-line-num new" data-linenumber="1466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1466
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<pre style="margin: 0;">+<span id="LC1466" class="line" lang="c"> <span class="kr" style="font-weight: 600;"><span class="idiff left">thread</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">template_index</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">template_index</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="old_line diff-line-num" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1459
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<td class="new_line diff-line-num" data-linenumber="1467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1467
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<pre style="margin: 0;"> <span id="LC1467" 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;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">threads</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1460
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<td class="new_line diff-line-num" data-linenumber="1468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1468
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<pre style="margin: 0;"> <span id="LC1468" class="line" lang="c"> <span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1461
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<td class="new_line diff-line-num" data-linenumber="1469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1469
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<pre style="margin: 0;"> <span id="LC1469" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1521" style="width: 35px; color: rgba(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="1529" style="width: 35px; color: rgba(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">@@ -1521,6 +1529,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<td class="old_line diff-line-num" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1521
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<td class="new_line diff-line-num" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1529
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<pre style="margin: 0;"> <span id="LC1529" 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;">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="old_line diff-line-num" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1522
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<td class="new_line diff-line-num" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1530
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<pre style="margin: 0;"> <span id="LC1530" 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;">next</span> <span 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="old_line diff-line-num" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1523
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<td class="new_line diff-line-num" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1531
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<pre style="margin: 0;"> <span id="LC1531" 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;">spin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sparse</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1532
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<pre style="margin: 0;">+<span id="LC1532" 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;">template_index</span><span class="p">;</span></span>
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1524
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<td class="new_line diff-line-num" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1533
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<pre style="margin: 0;"> <span id="LC1533" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1525
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<td class="new_line diff-line-num" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1534
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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Do local assemblies of fragments mapping to the same template */</span></span>
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<td class="old_line diff-line-num" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1526
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<td class="new_line diff-line-num" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1535
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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="c"> <span class="n" style="color: #333;">depth</span> <span 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="1550" style="width: 35px; color: rgba(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="1559" style="width: 35px; color: rgba(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">@@ -1550,6 +1559,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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1550
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<td class="new_line diff-line-num" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1559
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<pre style="margin: 0;"> <span id="LC1559" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><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="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</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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1551
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<td class="new_line diff-line-num" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1560
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<pre style="margin: 0;"> <span id="LC1560" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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1552
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<td class="new_line diff-line-num" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1561
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<pre style="margin: 0;"> <span id="LC1561" class="line" lang="c"> <span class="p">}</span></span>
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1562
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<pre style="margin: 0;">+<span id="LC1562" 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;">seq_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_in_no</span><span class="p">;</span></span>
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1553
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<td class="new_line diff-line-num" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1563
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<pre style="margin: 0;"> <span id="LC1563" 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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1554
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<td class="new_line diff-line-num" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1564
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<pre style="margin: 0;"> <span id="LC1564" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".name"</span><span class="p">);</span></span>
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1555
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<td class="new_line diff-line-num" data-linenumber="1565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1565
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<pre style="margin: 0;"> <span id="LC1565" class="line" lang="c"> <span class="n" style="color: #333;">name_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1593" style="width: 35px; color: rgba(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="1603" style="width: 35px; color: rgba(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">@@ -1593,7 +1603,6 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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1593
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<td class="new_line diff-line-num" data-linenumber="1603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1603
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<pre style="margin: 0;"> <span id="LC1603" class="line" lang="c"> <span class="n" style="color: #333;">printExtendedFeatures</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures_out</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1594
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<td class="new_line diff-line-num" data-linenumber="1604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1604
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<pre style="margin: 0;"> <span id="LC1604" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1595
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<td class="new_line diff-line-num" data-linenumber="1605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1605
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<pre style="margin: 0;"> <span id="LC1605" 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;">w_scores</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1596
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<td class="new_line diff-line-num old" data-linenumber="1606" style="width: 35px; color: rgba(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="LC1596" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1597
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<td class="new_line diff-line-num" data-linenumber="1606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1606
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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">progress</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1598
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<td class="new_line diff-line-num" data-linenumber="1607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1607
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<pre style="margin: 0;"> <span id="LC1607" class="line" lang="c"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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1599
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<td class="new_line diff-line-num" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1608
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<pre style="margin: 0;"> <span id="LC1608" 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;">"# Progress:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%3lu%%</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Nhits</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1628" style="width: 35px; color: rgba(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="1637" style="width: 35px; color: rgba(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">@@ -1628,10 +1637,11 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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1628
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1637
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<pre style="margin: 0;"> <span id="LC1637" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">xml</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1629
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1638
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<pre style="margin: 0;"> <span id="LC1638" class="line" lang="c"> <span class="n" style="color: #333;">newIterXML</span><span class="p">(</span><span class="n" style="color: #333;">xml_out</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">);</span></span>
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1630
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1639
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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="c"> <span class="p">}</span></span>
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1640
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<pre style="margin: 0;">+<span id="LC1640" class="line" lang="c"> </span>
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1631
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<td class="new_line diff-line-num" data-linenumber="1641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1641
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<pre style="margin: 0;"> <span id="LC1641" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Do assembly */</span></span>
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1632
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1642
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<pre style="margin: 0;"> <span id="LC1642" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//status |= assemblyPtr(aligned_assem, template, template_fragments, fileCount, frag_out, aligned, gap_align, qseq, header, matrix, points, NWmatrices);</span></span>
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<pre style="margin: 0;"> <span id="LC1643" 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="LC1634" 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;">t_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1644" 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;">t_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">t_len</span></span><span class="p">;</span></span>
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1645
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="c"> <span class="n" style="color: #333;">assembly_KMA_Ptr</span><span class="p">(</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">);</span></span>
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1646
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="c"> </span>
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1647
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<pre style="margin: 0;"> <span id="LC1647" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Depth, ID and coverage */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1718" style="width: 35px; color: rgba(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="1728" style="width: 35px; color: rgba(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">@@ -1718,9 +1728,6 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<pre style="margin: 0;"> <span id="LC1728" class="line" lang="c"> <span class="p">}</span></span>
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1729
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<pre style="margin: 0;"> <span id="LC1729" class="line" lang="c"> <span class="p">}</span></span>
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1730
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<pre style="margin: 0;"> <span id="LC1730" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC1721" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* destroy index */</span></span>
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<pre style="margin: 0;">-<span id="LC1722" class="line" lang="c"> <span class="n" style="color: #333;">hashMapCCI_destroy</span><span class="p">(</span><span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_index</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1723" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC1731" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Close files */</span></span>
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1732
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<pre style="margin: 0;"> <span id="LC1732" class="line" lang="c"> <span class="n" style="color: #333;">close</span><span class="p">(</span><span class="n" style="color: #333;">seq_in_no</span><span class="p">);</span></span>
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1733
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<pre style="margin: 0;"> <span id="LC1733" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">res_out</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#f568890dac40d04b36ce5786c44ac5704d31fe78"><strong>updateindex.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,7 +75,7 @@ int updateDBs_sparse(HashMap *templates, CompDNA *qseq, unsigned template, int M</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">template_slengths</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">template_ulengths</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</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="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">rc</span><span class="p">)</span> <span class="p">{</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* revers complement */</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* revers<span class="idiff left right">e</span> complement */</span></span>
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<pre style="margin: 0;"> <span id="LC79" 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="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"> <span class="n" style="color: #333;">comp_rc</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC81" 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">@@ -114,6 +114,9 @@ int updateDBs_sparse(HashMap *templates, CompDNA *qseq, unsigned template, int M</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prefix_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">comp_rc</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> </span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4"><strong>version.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,4 +17,4 @@</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * limitations under the License.</span></span>
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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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.<span class="idiff left right">19</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.<span class="idiff left right">22</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#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">@@ -144,11 +144,11 @@ void capIterXML(FILE *out, const int DB_size, const long unsigned seqsize, const</td>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"</Iteration></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hitXML</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlnScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alnStat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hitXML</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlnScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alnStat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Lock</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lock</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Lock</span><span class="p">;</span></span>
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num</span> <span 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="LC151" class="line" lang="c"> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lock</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Lock</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">W1s</span><span class="p">,</span> <span class="n" style="color: #333;">Us</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACGTN-"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -227,4 +227,17 @@ void hitXML(FILE *out, const int template, const char *template_name, const Aln</td>
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227
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">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</span><span class="s" style="color: #d14;"></Hit_hsps></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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228
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<pre style="margin: 0;"> <span id="LC228" 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;">"</Hit></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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229
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* here */</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> fprintf(stdout, "%s\n", template_name);</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> i = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> for(i = 0; i < aligned->len; i += 60) {</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> fprintf(stdout, "t:\t%.60s\n", aligned->t + i);</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> fprintf(stdout, "s:\t%.60s\n", aligned->s + i);</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> fprintf(stdout, "q:\t%.60s\n\n", aligned->q + i);</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> fprintf(stdout, "\n\n");</span></span>
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<pre style="margin: 0;">+<span id="LC241" 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="LC242" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/24c4ad423ca629e3f4c13de63d5e99e2c31a1ff8...049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef#dbf6fe29c92e85979d7bcdcde40617d9fcc417d0"><strong>xml.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">@@ -26,4 +26,4 @@ void closeCapXML(FILE *out);</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">newIterXML</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getEntropy</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned_assem_q</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">capIterXML</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">seqsize</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">readCounts</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p_value</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned_assem_q</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hitXML</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlnScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alnStat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hitXML</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Aln</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aligned</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlnScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alnStat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">);</span></span></pre>
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