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GitLab

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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/ed0e67e5ba00b0135bdde13331b3bc6d56024086">ed0e67e5</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-07-16T17:16:10+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.23</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/1ec2ebe565da30eb8382ddc07ffd66d63e2e1e72">1ec2ebe5</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-07-16T17:16:11+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update manpage

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/319fc038bff748bbc40f57e010f9fe2fa6adf4cc">319fc038</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-07-16T17:16:11+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry

</pre>

</li>

</ul>

<h4>11 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#56cfe3f38f05d51ac39678e58b5884d109593d0b">

compdna.c

</a>

</li>

<li class="file-stats">

<a href="#78dac453c30d3a83c1b0f89991ec896601711e1c">

compdna.h

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#a888ec8a19e2a0e07f82fa32481af66145f2a181">

debian/kma.1

</a>

</li>

<li class="file-stats">

<a href="#51702657d9880c43fadc322e37ff105d9816cb1b">

debian/kma_index.1

</a>

</li>

<li class="file-stats">

<a href="#b1e78e83886eae054a88c729cd12b63c3bf7b4ca">

debian/kma_shm.1

</a>

</li>

<li class="file-stats">

<a href="#e54b00420aceec6f11948d8c279380a68b99ba52">

makeindex.c

</a>

</li>

<li class="file-stats">

<a href="#e83be71f8bb7cb25f341010a5bf4d0baa9a967e5">

qseqs.c

</a>

</li>

<li class="file-stats">

<a href="#a8a38605a907c8cac583000616cd8c5f38ef0ff6">

qseqs.h

</a>

</li>

<li class="file-stats">

<a href="#7d21f6d2a4876afc9692035ab8b768c7552662bb">

seqparse.c

</a>

</li>

<li class="file-stats">

<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">

version.h

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="56cfe3f38f05d51ac39678e58b5884d109593d0b">

<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#56cfe3f38f05d51ac39678e58b5884d109593d0b"><strong>compdna.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(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="24" style="width: 35px; color: rgba(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">@@ -24,7 +24,7 @@</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 "qseqs.h"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdnuc.h"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(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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<td class="new_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">allocComp</span><span class="p">(</span><span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="27" 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="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">allocComp</span><span class="p">(</span><span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c">     </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c">     <span class="n" style="color: #333;">compressor</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c">     <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">31</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="78dac453c30d3a83c1b0f89991ec896601711e1c">

<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#78dac453c30d3a83c1b0f89991ec896601711e1c"><strong>compdna.h</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(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="22" style="width: 35px; color: rgba(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">@@ -22,16 +22,16 @@</td>

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef COMPDNA</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">compDNA</span> <span class="n" style="color: #333;">CompDNA</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">compDNA</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(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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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(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="LC25" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">seqlen</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(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="LC26" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">complen</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="25" 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="LC25" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">seqlen</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="26" 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="LC26" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="27" 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="LC27" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">complen</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="p">};</span></span>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define COMPDNA 1</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">allocComp</span><span class="p">(</span><span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="34" 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="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">allocComp</span><span class="p">(</span><span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">freeComp</span><span class="p">(</span><span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">setComp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">destroyComp</span><span class="p">(</span><span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">);</span></span>

</pre>

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<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">kma (1.3.2<span class="idiff left right">2</span>-1) UNRELEASED; urgency=medium</span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kma (1.3.2<span class="idiff left right">3</span>-1) UNRELEASED; urgency=medium</span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">  * New upstream version 1.3.2<span class="idiff left right">2</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version 1.3.2<span class="idiff left right">3</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  * d/*.1: Update Manpages</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">  * d/p/blhc.patch: Propagate hardening flags to fix blhc</span>

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>

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</li>

<li id="a888ec8a19e2a0e07f82fa32481af66145f2a181">

<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#a888ec8a19e2a0e07f82fa32481af66145f2a181"><strong>debian/kma.1</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH KMA "1" "Ju<span class="idiff left">ne</span> 2021" "kma 1.3.2<span class="idiff right">2</span>" "User Commands"</span>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH KMA "1" "Ju<span class="idiff left">ly</span> 2021" "kma 1.3.2<span class="idiff right">3</span>" "User Commands"</span>

</pre>

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">kma \- maps and/or aligns raw reads to a template database</span>

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">.IP</span>

</pre>

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7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">KMA\-1.3.2<span class="idiff left right">2</span> maps and/or aligns raw reads to a template database.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">KMA\-1.3.2<span class="idiff left right">3</span> maps and/or aligns raw reads to a template database.</span>

</pre>

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8

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">.TP</span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Options:</span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Desc:                                   Default:</span>

</pre>

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</li>

<li id="51702657d9880c43fadc322e37ff105d9816cb1b">

<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#51702657d9880c43fadc322e37ff105d9816cb1b"><strong>debian/kma_index.1</strong></a>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH KMA_INDEX "1" "Ju<span class="idiff left">ne</span> 2021" "kma_index 1.3.2<span class="idiff right">2</span>" "User Commands"</span>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH KMA_INDEX "1" "Ju<span class="idiff left">ly</span> 2021" "kma_index 1.3.2<span class="idiff right">3</span>" "User Commands"</span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">kma_index \- creates the databases needed to run KMA, from a list of fasta files given</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>

</pre>

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<br>

</li>

<li id="b1e78e83886eae054a88c729cd12b63c3bf7b4ca">

<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#b1e78e83886eae054a88c729cd12b63c3bf7b4ca"><strong>debian/kma_shm.1</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH KMA_SHM "1" "Ju<span class="idiff left">ne</span> 2021" "kma_shm 1.3.2<span class="idiff right">2</span>" "User Commands"</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH KMA_SHM "1" "Ju<span class="idiff left">ly</span> 2021" "kma_shm 1.3.2<span class="idiff right">3</span>" "User Commands"</span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">kma_shm \- sets up a shared database (sysV) for mapping with KMA</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>

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</li>

<li id="e54b00420aceec6f11948d8c279380a68b99ba52">

<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#e54b00420aceec6f11948d8c279380a68b99ba52"><strong>makeindex.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" style="width: 35px; color: rgba(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="95" style="width: 35px; color: rgba(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">@@ -95,7 +95,7 @@ void makeDB(HashMap *templates, int kmerindex, char **inputfiles, int fileCount,</td>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c">                     <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">FileBuffgetFsa</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">trans</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c">                             <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">compressor</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c">                                     <span class="n" style="color: #333;">freeComp</span><span class="p">(</span><span class="n" style="color: #333;">compressor</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="c">                                     <span class="n" style="color: #333;">allocComp</span><span class="p">(</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">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="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="LC98" class="line" lang="c">                                     <span class="n" style="color: #333;">allocComp</span><span class="p">(</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">size</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c">                             <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c">                            <span class="n" style="color: #333;">bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compDNAref</span><span class="p">(</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c">                            </span>

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<li id="e83be71f8bb7cb25f341010a5bf4d0baa9a967e5">

<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#e83be71f8bb7cb25f341010a5bf4d0baa9a967e5"><strong>qseqs.c</strong></a>

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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 "pherror.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 "qseqs.h"</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">setQseqs</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">setQseqs</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c">     </span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c">     <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c">     </span>

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<li id="a8a38605a907c8cac583000616cd8c5f38ef0ff6">

<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#a8a38605a907c8cac583000616cd8c5f38ef0ff6"><strong>qseqs.h</strong></a>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef QSEQS</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">qseqs</span> <span class="n" style="color: #333;">Qseqs</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">qseqs</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define QSEQS 1</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* initialize Qseqs */</span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">setQseqs</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">setQseqs</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* destroy Qseqs */</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">destroyQseqs</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">insertKmerBound</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span><span class="p">);</span></span></pre>

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<br>

</li>

<li id="7d21f6d2a4876afc9692035ab8b768c7552662bb">

<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#7d21f6d2a4876afc9692035ab8b768c7552662bb"><strong>seqparse.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">@@ -66,7 +66,7 @@ int openAndDetermine(FileBuff *inputfile, char *filename) {</td>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">FileBuffgetFsa</span><span class="p">(</span><span class="n" style="color: #333;">FileBuff</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trans</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c">     </span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buff</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(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="LC69" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">avail</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">avail</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c">     </span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c">     <span class="cm" style="color: #998; font-style: italic;">/* init */</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c">     <span class="n" style="color: #333;">avail</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bytes</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" style="width: 35px; color: rgba(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="161" style="width: 35px; color: rgba(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">@@ -161,7 +161,7 @@ int FileBuffgetFsa(FileBuff *src, Qseqs *header, Qseqs *qseq, char *trans) {</td>

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161

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">FileBuffgetFsaSeq</span><span class="p">(</span><span class="n" style="color: #333;">FileBuff</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trans</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c">    </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buff</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

164

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<td class="new_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(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="LC164" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">avail</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="164" 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="LC164" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">avail</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

165

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<td class="new_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c">    </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* init */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c">    <span class="n" style="color: #333;">avail</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bytes</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="241" style="width: 35px; color: rgba(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="241" style="width: 35px; color: rgba(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">@@ -241,7 +241,7 @@ int FileBuffgetFsaSeq(FileBuff *src, Qseqs *qseq, char *trans) {</td>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">FileBuffgetFq</span><span class="p">(</span><span class="n" style="color: #333;">FileBuff</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trans</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c">    </span>

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<td class="old_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buff</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="244" style="width: 35px; color: rgba(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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<td class="new_line diff-line-num old" data-linenumber="244" style="width: 35px; color: rgba(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="LC244" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">avail</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="244" 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="LC244" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">avail</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c">    </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* init */</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c">    <span class="n" style="color: #333;">avail</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bytes</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="396" style="width: 35px; color: rgba(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="396" style="width: 35px; color: rgba(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">@@ -396,7 +396,7 @@ int FileBuffgetFq(FileBuff *src, Qseqs *header, Qseqs *qseq, Qseqs *qual, char *</td>

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<td class="old_line diff-line-num" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

396

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<td class="new_line diff-line-num" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

396

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">FileBuffgetFqSeq</span><span class="p">(</span><span class="n" style="color: #333;">FileBuff</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trans</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

397

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<td class="new_line diff-line-num" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

397

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c">    </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

398

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<td class="new_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

398

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buff</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

399

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<td class="new_line diff-line-num old" data-linenumber="399" style="width: 35px; color: rgba(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="LC399" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">avail</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="399" 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">

399

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">avail</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

400

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<td class="new_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

400

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="c">    </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

401

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<td class="new_line diff-line-num" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

401

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* init */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

402

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<td class="new_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

402

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="c">    <span class="n" style="color: #333;">avail</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bytes</span><span class="p">;</span></span>

</pre>

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</table>

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</li>

<li id="2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">

<a href="https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4"><strong>version.h</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(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="17" style="width: 35px; color: rgba(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">@@ -17,4 +17,4 @@</td>

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17

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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" 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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<td class="new_line diff-line-num old" 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">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.2<span class="idiff left right">2</span>"</span></span></pre>

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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" 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">

20

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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 "1.3.2<span class="idiff left right">3</span>"</span></span></pre>

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