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<h3>
Steffen Möller 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/18e38cc75163339bc44ef228180b9b1f62a3bee1">18e38cc7</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T15:00:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.16</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/commit/cbfc50a6a368b361919bdb7280671e5823dc9ee9">cbfc50a6</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T15:00:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/commit/669933a168f58a93429621820ff4ad96fb58d25c">669933a1</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T15:00:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.2.16'
Update to upstream version '1.2.16'
with Debian dir 4b333b64b71a29351ce58f24bf96a760d354282b</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/commit/dfa0d30d30c830de0d9ab479e37525fe1457b69f">dfa0d30d</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T15:00:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Repository.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/commit/d6256546f2607e48f3b102a45fbb211d8a491620">d6256546</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T15:00:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<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="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#5bb411548ec4b39482e6de83d3ad98f29b1162b1">
kma.c
</a>
</li>
<li class="file-stats">
<a href="#406e031b8824ea26ae0bf4d7579a1d89e3fb5906">
main.c
</a>
</li>
<li class="file-stats">
<a href="#97e3379ce2e33418ea5b83d3faaf35326b973d41">
nw.c
</a>
</li>
<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
<a href="https://salsa.debian.org/med-team/kma/compare/7f765c85bf8713aef54ba0c142a3d1827e8d0fd7...d6256546f2607e48f3b102a45fbb211d8a491620#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40"><strong>align.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="601" style="width: 35px; color: rgba(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="601" style="width: 35px; color: rgba(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">@@ -601,6 +601,7 @@ AlnScore KMA_score(const HashMap_index *template_index, const unsigned char *qse</td>
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<td class="diff-line-num old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
601
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<td class="diff-line-num new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
601
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_score</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
602
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<td class="diff-line-num new_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
602
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<pre style="margin: 0;"> <span id="LC602" 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 old_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
603
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<td class="diff-line-num new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="c"> <span class="n" style="color: #333;">NWstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NW_band_score</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">t_s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">t_s</span><span class="p">,</span> <span class="n" style="color: #333;">t_e</span><span class="p">,</span> <span class="n" style="color: #333;">q_s</span><span class="p">,</span> <span class="n" style="color: #333;">q_e</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//NWstat = NW_score(template_index->seq, qseq, -1 - (t_s == 0), t_s, t_e, q_s, q_e, matrices, t_len);</span></span>
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604
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<td class="diff-line-num new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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605
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<td class="diff-line-num new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
606
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<td class="diff-line-num new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWstat</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<li id="99bf70d606be11e0793b7e3ba6c29182326341d6">
<a href="https://salsa.debian.org/med-team/kma/compare/7f765c85bf8713aef54ba0c142a3d1827e8d0fd7...d6256546f2607e48f3b102a45fbb211d8a491620#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">@@ -18,6 +18,7 @@</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _XOPEN_SOURCE 600</span></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;">#include <ctype.h></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <limits.h></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></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">@@ -167,7 +168,7 @@ unsigned char baseCaller(unsigned char bestNuc, unsigned char tNuc, int bestScor</td>
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167
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168
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<pre style="margin: 0;"> <span id="LC168" 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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168
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Use MnNemars test to test significance of the base call */</span></span>
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169
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">significantBase</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">depthUpdate</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</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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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestNuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tNuc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestNuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tNuc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'-'</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">bestScore</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">depthUpdate</span></span><span class="p">)</span> <span class="p">{</span></span>
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171
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">bestNuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">;</span></span>
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172
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173
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<pre style="margin: 0;"> <span id="LC173" 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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173
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">bestNuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tolower</span><span class="p">(</span><span class="n" style="color: #333;">bestNuc</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(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="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -213,7 +214,7 @@ unsigned char nanoCaller(unsigned char bestNuc, unsigned char tNuc, int bestScor</td>
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213
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214
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<pre style="margin: 0;"> <span id="LC214" 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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214
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Use MC Neymars test to test significance of the base call */</span></span>
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215
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">significantBase</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">depthUpdate</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</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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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestNuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tNuc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestNuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tNuc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'-'</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">bestScore</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">depthUpdate</span></span><span class="p">)</span> <span class="p">{</span></span>
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217
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">bestBaseScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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218
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219
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<pre style="margin: 0;"> <span id="LC219" 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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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219
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestBaseScore</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">calls</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">j</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="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -337,10 +338,7 @@ void * assemble_KMA_threaded(void *arg) {</td>
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337
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC339" 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;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">free</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;">assmb</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">matrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">assmb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</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="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Assembly</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC341" 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;">matrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">assmb</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC341" 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;">assmb</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;">matrix</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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Assembly</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* cpy template seq */</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">@@ -473,7 +471,9 @@ void * assemble_KMA_threaded(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">aln_len</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</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;">5</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Template gap, insertion</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">pos</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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</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="LC474" 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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="c"> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">USHRT_MAX</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="c"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC479" 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">@@ -517,8 +517,8 @@ void * assemble_KMA_threaded(void *arg) {</td>
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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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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518
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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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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519
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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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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520
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="c"> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myBias</span><span class="p">;</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="c"> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span><span class="o" style="font-weight: 600;"><span class="idiff left right">++</span></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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myBias</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">USHRT_MAX</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">myBias</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">USHRT_MAX</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="c"> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC524" 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">@@ -528,7 +528,9 @@ void * assemble_KMA_threaded(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="c"> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="c"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">next</span><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="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="c"> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</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="LC531" 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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]])</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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">USHRT_MAX</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="c"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -651,10 +653,10 @@ void * assemble_KMA_threaded(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* call query */</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="c"> <span class="n" style="color: #333;">bestNuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">5</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="c"> <span class="n" style="color: #333;">depthUpdate</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="LC657" 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="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="c"> <span class="n" style="color: #333;">bestNuc</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="LC657" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">assembly</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">counts</span></span><span class="p"><span class="idiff">[</span></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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<pre style="margin: 0;">+<span id="LC658" class="line" lang="c"> <span class="n" style="color: #333;">depthUpdate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">bestScore</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC659" 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="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC660" 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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</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="LC661" 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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="c"> <span class="n" style="color: #333;">bestNuc</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -666,9 +668,9 @@ void * assemble_KMA_threaded(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check for minor base call */</span></span>
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<pre style="margin: 0;"> <span id="LC669" 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;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">depthUpdate</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestNuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="c"> <span class="n" style="color: #333;">bestBaseScore</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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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="c"> <span class="n" style="color: #333;">bestBaseScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">assembly</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">counts</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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672
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="c"> <span class="n" style="color: #333;">bestNuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC671" 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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left right">5</span></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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673
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<pre style="margin: 0;">+<span id="LC673" 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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left right">4</span></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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674
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestBaseScore</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</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="LC675" class="line" lang="c"> <span class="n" style="color: #333;">bestBaseScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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676
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="c"> <span class="n" style="color: #333;">bestNuc</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="948" style="width: 35px; color: rgba(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">@@ -948,7 +950,9 @@ void * assemble_KMA_dense_threaded(void *arg) {</td>
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<pre style="margin: 0;"> <span id="LC950" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* diff */</span></span>
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951
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<pre style="margin: 0;"> <span id="LC951" class="line" lang="c"> <span class="k" style="font-weight: 600;">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;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">aln_len</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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952
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<pre style="margin: 0;"> <span id="LC952" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</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;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="c"> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" 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;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="c"> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">aligned</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">USHRT_MAX</span><span class="p">;</span> </span>
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="c"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">assembly</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="n" style="color: #333;">next</span><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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<pre style="margin: 0;"> <span id="LC958" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/compare/7f765c85bf8713aef54ba0c142a3d1827e8d0fd7...d6256546f2607e48f3b102a45fbb211d8a491620#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kma (1.2.16-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Set upstream metadata fields: Repository.</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"> -- Steffen Moeller <moeller@debian.org> Sat, 30 Nov 2019 16:00:16 +0100</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 (1.2.15-1) 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="LC11" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/kma/compare/7f765c85bf8713aef54ba0c142a3d1827e8d0fd7...d6256546f2607e48f3b102a45fbb211d8a491620#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Author: Philip T. L. C. Clausen and Frank M. Aarestrup and Ole Lund</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Rapid and precise alignment of raw reads against redundant databases</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> with KMA</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Journal: BMC Bioinformatics</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Year: 2018</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Volume: 19</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Pages: 307</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> DOI: 10.1186/s12859-018-2336-6</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> PMID: 30157759</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116485/</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> eprint: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116485/\</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> pdf/12859_2018_Article_2336.pdf"</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Author: Philip T. L. C. Clausen and Frank M. Aarestrup and Ole Lund</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Rapid and precise alignment of raw reads against redundant databases</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> with KMA</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Journal: BMC Bioinformatics</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Year: 2018</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Volume: 19</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Pages: 307</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> DOI: 10.1186/s12859-018-2336-6</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> PMID: 30157759</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116485/</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> eprint: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116485/pdf/12859_2018_Article_2336.pdf"</span>
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15
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Registry:</span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> - Name: OMICtools</span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> Entry: OMICS_31606</span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> - Name: bio.tools</span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> Entry: kma</span></pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">- Name: OMICtools</span>
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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Entry: OMICS_31606</span>
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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">- Name: bio.tools</span>
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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(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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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> Entry: NA</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Entry: kma</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Repository: https://bitbucket.org/genomicepidemiology/kma</span></pre>
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<a href="https://salsa.debian.org/med-team/kma/compare/7f765c85bf8713aef54ba0c142a3d1827e8d0fd7...d6256546f2607e48f3b102a45fbb211d8a491620#5bb411548ec4b39482e6de83d3ad98f29b1162b1"><strong>kma.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="164" style="width: 35px; color: rgba(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">@@ -164,6 +164,7 @@ static void helpMessage(int exeStatus) {</td>
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164
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-transversion</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for transversion</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-2</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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165
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-cge</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Set CGE penalties and rewards</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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166
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-t</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Number of threads</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-c</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Citation</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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167
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-v</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Version</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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168
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-h</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Shows this help message</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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169
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="789" style="width: 35px; color: rgba(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="790" style="width: 35px; color: rgba(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">@@ -789,6 +790,9 @@ int kma_main(int argc, char *argv[]) {</td>
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789
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<td class="diff-line-num new_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-v"</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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790
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<td class="diff-line-num new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"KMA-%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">KMA_VERSION</span><span class="p">);</span></span>
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791
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-c"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"Philip T.L.C. Clausen, Frank M. Aarestrup & Ole Lund, </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Rapid and precise alignment of raw reads against redundant databases with KMA</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, BMC Bioinformatics, 2018;19:307.</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 new new_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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792
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-h"</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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793
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="c"> <span class="n" style="color: #333;">helpMessage</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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798
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<pre style="margin: 0;"> <span id="LC798" 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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<a href="https://salsa.debian.org/med-team/kma/compare/7f765c85bf8713aef54ba0c142a3d1827e8d0fd7...d6256546f2607e48f3b102a45fbb211d8a491620#406e031b8824ea26ae0bf4d7579a1d89e3fb5906"><strong>main.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">@@ -24,14 +24,18 @@</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "seq2fasta.h"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "update.h"</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">helpmessage</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">helpmessage</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">FILE</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">out</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"> <span class="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;">"# For help please use:</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="LC30" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kma -h</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="LC31" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kma index -h</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="LC32" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kma shm -h</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="LC33" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kma seq2fasta -h</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="LC34" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kma update -h</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="LC29" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# KMA enables alignment towards databases, using two k-mer mapping steps and one alignment step.</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="LC30" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Options are:"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Desc:"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"Alignment and mapping"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"index"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Indexing of databases"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"shm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Shared memory"</span><span class="p">);</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"seq2fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Conversion of database to fasta"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"update"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Update database to current version"</span><span class="p">);</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Citation"</span><span class="p">);</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-v"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Version"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-h"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Help on alignment and mapping"</span><span class="p">);</span></span>
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35
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39
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<pre style="margin: 0;"> <span id="LC39" 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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36
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="p">}</span></span>
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37
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" style="width: 35px; color: rgba(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="56" style="width: 35px; color: rgba(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">@@ -52,11 +56,10 @@ int main(int argc, char *argv[]) {</td>
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52
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">update_main</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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53
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<td class="diff-line-num new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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54
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<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Invalid option:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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55
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<td class="diff-line-num new_line old" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">helpmessage</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">helpmessage</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">stderr</span></span><span class="p">);</span></span>
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56
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="p">}</span></span>
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57
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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
61
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<pre style="margin: 0;"> <span id="LC61" 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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58
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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Too few arguments handed</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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59
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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">helpmessage</span><span class="p">();</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">helpmessage</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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60
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">status</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/kma/compare/7f765c85bf8713aef54ba0c142a3d1827e8d0fd7...d6256546f2607e48f3b102a45fbb211d8a491620#97e3379ce2e33418ea5b83d3faaf35326b973d41"><strong>nw.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -556,7 +556,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">D_prev</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="LC557" class="line" lang="c"> <span class="n" style="color: #333;">pos</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="c"> <span class="n" style="color: #333;">pos</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span 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="LC559" class="line" lang="c"> <span class="n" style="color: #333;">q_pos</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="LC559" class="line" lang="c"> <span class="n" style="color: #333;">q_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">en</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/compare/7f765c85bf8713aef54ba0c142a3d1827e8d0fd7...d6256546f2607e48f3b102a45fbb211d8a491620#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4"><strong>version.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,4 +17,4 @@</td>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.2.1<span class="idiff left right">5</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.2.1<span class="idiff left right">6</span>"</span></span></pre>
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