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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/6ad1fa9b0632751360e50a82890a466eea022836">6ad1fa9b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-18T11:46:37+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/51a0802d7b4de7202aba09915798d7a01ebcda0b">51a0802d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-18T11:46:38+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.5</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/148042afaab15b6c633daf792f1a5942647687fd">148042af</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-10-18T11:46:39+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.3.5'
Update to upstream version '1.3.5'
with Debian dir 9f0281d6c1dde597c9b18edbda759bdc73ce1dc6</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/2daa16aa15b17f0954258dfabd86db2b27cefce7">2daa16aa</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-18T11:46:53+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#5bb411548ec4b39482e6de83d3ad98f29b1162b1">
kma.c
</a>
</li>
<li class="file-stats">
<a href="#ca9efd475143efe0a1b0464c67f49900d98ca75a">
runkma.c
</a>
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<li class="file-stats">
<a href="#f80652dda49a7117428c0f92935664fc8cd4e2d1">
spltdb.c
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<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kma/-/compare/e171acafe77507a366fd399ce51ab14c69664822...2daa16aa15b17f0954258dfabd86db2b27cefce7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kma (1.3.5-1) 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"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Sun, 18 Oct 2020 11:46:53 +0530</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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1
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">kma (1.3.4-1) unstable; urgency=medium</span>
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2
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team upload.</span>
</pre>
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<li id="5bb411548ec4b39482e6de83d3ad98f29b1162b1">
<a href="https://salsa.debian.org/med-team/kma/-/compare/e171acafe77507a366fd399ce51ab14c69664822...2daa16aa15b17f0954258dfabd86db2b27cefce7#5bb411548ec4b39482e6de83d3ad98f29b1162b1"><strong>kma.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="530" style="width: 35px; color: rgba(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="530" style="width: 35px; color: rgba(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">@@ -530,6 +530,7 @@ int kma_main(int argc, char *argv[]) {</td>
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530
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="c"> <span class="n" style="color: #333;">alnToMatPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnToMatDense</span><span class="p">;</span></span>
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531
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="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;">"-sasm"</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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532
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="c"> <span class="n" style="color: #333;">assembly_KMA_Ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">skip_assemble_KMA</span><span class="p">;</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="c"> <span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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533
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534
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<pre style="margin: 0;"> <span id="LC534" 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;">"-matrix"</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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534
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535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="c"> <span class="n" style="color: #333;">print_matrix</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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535
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536
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<pre style="margin: 0;"> <span id="LC536" 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;">"-a"</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -635,7 +636,7 @@ int kma_main(int argc, char *argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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637
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="c"> <span class="n" style="color: #333;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exeBasic</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Invalid argument at </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-<span class="idiff left right">ID</span></span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Invalid argument at </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-<span class="idiff left right">bcd</span></span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/e171acafe77507a366fd399ce51ab14c69664822...2daa16aa15b17f0954258dfabd86db2b27cefce7#ca9efd475143efe0a1b0464c67f49900d98ca75a"><strong>runkma.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2385,14 +2385,19 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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<pre style="margin: 0;"> <span id="LC2385" class="line" lang="c"> <span class="n" style="color: #333;">cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2386" class="line" lang="c"> <span class="n" style="color: #333;">q_cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">aln_len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2387" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2388
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<pre style="margin: 0;">-<span id="LC2388" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2388" class="line" lang="c"> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2389" class="line" lang="c"> <span class="n" style="color: #333;">q_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2390" class="line" lang="c"> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">depth</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2391" class="line" lang="c"> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2392" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">aln_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2393" class="line" lang="c"> <span class="n" style="color: #333;">cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2394" class="line" lang="c"> <span class="n" style="color: #333;">q_cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2395
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<pre style="margin: 0;"> <span id="LC2395" class="line" lang="c"> <span class="p">}</span></span>
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2396
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<pre style="margin: 0;"> <span id="LC2396" class="line" lang="c"> </span>
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2392
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2397
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<pre style="margin: 0;"> <span id="LC2397" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">xml</span><span class="p">)</span> <span class="p">{</span></span>
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2398
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<pre style="margin: 0;"> <span id="LC2398" class="line" lang="c"> <span class="n" style="color: #333;">capIterXML</span><span class="p">(</span><span class="n" style="color: #333;">xml_out</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">seqin_size</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">],</span> <span class="n" style="color: #333;">p_value</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">);</span></span>
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2394
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2399
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<pre style="margin: 0;"> <span id="LC2399" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC2395" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">id</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">0</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">id</span></span><span class="p">)</span> <span class="p">{</span></span>
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2400
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<pre style="margin: 0;">+<span id="LC2400" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="p">{</span></span>
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2401
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<pre style="margin: 0;"> <span id="LC2401" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Output result */</span></span>
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2397
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2402
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<pre style="margin: 0;"> <span id="LC2402" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">res_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-12s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8ld</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8u</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%4.1e</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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2398
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2403
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<pre style="margin: 0;"> <span id="LC2403" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">cover</span><span class="p">,</span> <span class="n" style="color: #333;">q_id</span><span class="p">,</span> <span class="n" style="color: #333;">q_cover</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">q_value</span><span class="p">,</span> <span class="n" style="color: #333;">p_value</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2427" style="width: 35px; color: rgba(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="2432" style="width: 35px; color: rgba(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">@@ -2427,7 +2432,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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2427
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2432
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<pre style="margin: 0;"> <span id="LC2432" class="line" lang="c"> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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2428
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2433
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<pre style="margin: 0;"> <span id="LC2433" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</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;">aln_len</span><span class="p">;</span></span>
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2429
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2434
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<pre style="margin: 0;"> <span id="LC2434" class="line" lang="c"> <span class="n" style="color: #333;">cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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2430
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<pre style="margin: 0;">-<span id="LC2430" class="line" lang="c"> <span class="n" style="color: #333;">q_cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">100</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t_len</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">aln_len</span></span><span class="p">;</span></span>
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2435
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<pre style="margin: 0;">+<span id="LC2435" class="line" lang="c"> <span class="n" style="color: #333;">q_cover</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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2431
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2436
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<pre style="margin: 0;"> <span id="LC2436" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">res_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-12s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8ld</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8u</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%4.1e</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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2437
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<pre style="margin: 0;"> <span id="LC2437" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">cover</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">q_cover</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">q_value</span><span class="p">,</span> <span class="n" style="color: #333;">p_value</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2438" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendedFeatures</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1633,14 +1633,19 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<pre style="margin: 0;"> <span id="LC1633" class="line" lang="c"> <span class="n" style="color: #333;">q_cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">aln_len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1634" 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="LC1635" class="line" lang="c"> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1636" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1636" class="line" lang="c"> <span class="n" style="color: #333;">q_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1637" class="line" lang="c"> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">depth</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1638" class="line" lang="c"> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1639" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">aln_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1640" class="line" lang="c"> <span class="n" style="color: #333;">cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">t_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1641" class="line" lang="c"> <span class="n" style="color: #333;">q_cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1642" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1643" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">xml</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="c"> <span class="n" style="color: #333;">capIterXML</span><span class="p">(</span><span class="n" style="color: #333;">xml_out</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">seqin_size</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">readCounts</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">],</span> <span class="n" style="color: #333;">p_value</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="c"> <span class="p">}</span></span>
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1647
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<pre style="margin: 0;"> <span id="LC1647" class="line" lang="c"> </span>
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1643
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<pre style="margin: 0;">-<span id="LC1643" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">id</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">0</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">id</span></span><span class="p">)</span> <span class="p">{</span></span>
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1648
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<pre style="margin: 0;">+<span id="LC1648" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="p">{</span></span>
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1644
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1649
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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Output result */</span></span>
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1645
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1650
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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">res_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-12s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8ld</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8u</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%4.1e</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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1646
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1651
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<pre style="margin: 0;"> <span id="LC1651" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">cover</span><span class="p">,</span> <span class="n" style="color: #333;">q_id</span><span class="p">,</span> <span class="n" style="color: #333;">q_cover</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">q_value</span><span class="p">,</span> <span class="n" style="color: #333;">p_value</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/e171acafe77507a366fd399ce51ab14c69664822...2daa16aa15b17f0954258dfabd86db2b27cefce7#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4"><strong>version.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,4 +17,4 @@</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.<span class="idiff left right">4</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.<span class="idiff left right">5</span>"</span></span></pre>
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