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<h3>

Nilesh Patra pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/c5c372bbfad911d7fe80e3aa1645d2e2572f6fdc">c5c372bb</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-21T17:39:21+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.7</pre>

</li>

</ul>

<h4>5 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#0b5ffc8f7b4dae4c15ab46909e3b4189a01fb548">

hashmapcci.c

</a>

</li>

<li class="file-stats">

<a href="#fe684ebf71f22762560b62973b5be5098b7ce2a4">

hashmapcci.h

</a>

</li>

<li class="file-stats">

<a href="#ca9efd475143efe0a1b0464c67f49900d98ca75a">

runkma.c

</a>

</li>

<li class="file-stats">

<a href="#f80652dda49a7117428c0f92935664fc8cd4e2d1">

spltdb.c

</a>

</li>

<li class="file-stats">

<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">

version.h

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="0b5ffc8f7b4dae4c15ab46909e3b4189a01fb548">

<a href="https://salsa.debian.org/med-team/kma/-/commit/c5c372bbfad911d7fe80e3aa1645d2e2572f6fdc#0b5ffc8f7b4dae4c15ab46909e3b4189a01fb548"><strong>hashmapcci.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" style="width: 35px; color: rgba(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="93" style="width: 35px; color: rgba(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">@@ -93,7 +93,7 @@ void hashMapCCI_destroy(HashMapCCI *dest) {</td>

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<td class="diff-line-num old_line" data-linenumber="93" style="width: 35px; color: rgba(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="LC93" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(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="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(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="LC94" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">hashMapCCI_get</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shifter</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c">     </span>

</pre>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="96" 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="LC96" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(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="LC97" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chain</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c">     </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(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="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(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="LC99" class="line" lang="c">     <span class="cm" style="color: #998; font-style: italic;">/* get hash */</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="120" style="width: 35px; color: rgba(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="120" style="width: 35px; color: rgba(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">@@ -120,7 +120,7 @@ int hashMapCCI_get(const HashMapCCI *dest, long unsigned key, unsigned shifter)</td>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">hashMapCCI_get_bound</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shifter</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c">    </span>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="124" 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="LC123" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">apos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chain</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c">    </span>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(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="LC126" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* get hash */</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(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="148" style="width: 35px; color: rgba(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">@@ -148,7 +148,7 @@ int hashMapCCI_get_bound(const HashMapCCI *dest, long unsigned key, int min, int</td>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC149" 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="nf" style="color: #900; font-weight: 600;">hashMapCCI_getDubPos</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shifter</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(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="LC151" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="152" 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="LC151" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(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="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(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="LC152" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chain</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" style="width: 35px; color: rgba(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="LC153" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(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="LC154" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* check input */</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="198" style="width: 35px; color: rgba(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="198" style="width: 35px; color: rgba(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">@@ -198,8 +198,7 @@ int defragChain(HashMapCCI *dest, int size, int shifter) {</td>

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<td class="diff-line-num old_line" data-linenumber="198" style="width: 35px; color: rgba(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="LC198" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* defragmentize the chains to make space for new chain, return 0 on failure */</span></span>

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<td class="diff-line-num new_line" data-linenumber="199" style="width: 35px; color: rgba(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="LC199" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newsize</span><span class="p">,</span> <span class="n" style="color: #333;">cci_size</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">newpos</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">fulldefrag</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="200" style="width: 35px; color: rgba(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="LC200" 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;">newchain</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(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="LC201" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">ipos</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="202" style="width: 35px; color: rgba(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="LC202" 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="n" style="color: #333;">kmer</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="203" 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="LC201" 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="n" style="color: #333;">ipos</span><span class="p">,</span> <span class="n" style="color: #333;">kmer</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c">    </span>

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<td class="diff-line-num new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* check if chain is available */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(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="diff-line-num new_line" data-linenumber="204" style="width: 35px; color: rgba(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="LC204" 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="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cci_avail</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="276" style="width: 35px; color: rgba(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="275" style="width: 35px; color: rgba(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">@@ -276,7 +275,8 @@ int defragChain(HashMapCCI *dest, int size, int shifter) {</td>

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<td class="diff-line-num old_line" data-linenumber="276" style="width: 35px; color: rgba(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="diff-line-num new_line" data-linenumber="275" style="width: 35px; color: rgba(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="LC275" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">newChain</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newpos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">kmer</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">shifter</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* add new chain to hashmap */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="279" style="width: 35px; color: rgba(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="LC279" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chain</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="278" 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="LC278" 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;">chain</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="279" 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="LC279" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="280" style="width: 35px; color: rgba(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="LC280" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="281" style="width: 35px; color: rgba(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="diff-line-num new_line" data-linenumber="281" style="width: 35px; color: rgba(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="LC281" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cci_avail</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c">            <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cci_next</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="307" style="width: 35px; color: rgba(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="307" style="width: 35px; color: rgba(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">@@ -307,7 +307,7 @@ int newChain(HashMapCCI *dest, int pos, int newpos, long unsigned kmer, int shif</td>

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<td class="diff-line-num new_line" data-linenumber="307" style="width: 35px; color: rgba(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="LC307" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">extendChain</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chainpos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newpos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">kmer</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">shifter</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="309" style="width: 35px; color: rgba(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="diff-line-num new_line" data-linenumber="309" style="width: 35px; color: rgba(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="LC309" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">dup</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">newchain</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="310" style="width: 35px; color: rgba(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="diff-line-num new_line old" data-linenumber="310" style="width: 35px; color: rgba(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="LC310" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="c">    </span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="c">    <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chainpos</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="313" style="width: 35px; color: rgba(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="LC313" class="line" lang="c">    <span class="n" style="color: #333;">chain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chain</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -397,7 +397,7 @@ int extendChain(HashMapCCI *dest, int chainpos, int newpos, long unsigned kmer,</td>

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<td class="diff-line-num old_line" 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">

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hashMapCCI_add</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newpos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shifter</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c">    </span>

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<td class="diff-line-num old_line" data-linenumber="399" style="width: 35px; color: rgba(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="LC399" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">index_ptr</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC400" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c">    </span>

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<td class="diff-line-num old_line" 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">

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="403" style="width: 35px; color: rgba(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="LC403" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* likely undefined region */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="424" style="width: 35px; color: rgba(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="424" style="width: 35px; color: rgba(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">@@ -424,7 +424,7 @@ void hashMapCCI_add_thread(HashMapCCI *dest, long unsigned key, int newpos, unsi</td>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="c">    </span>

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<td class="diff-line-num old_line" data-linenumber="425" style="width: 35px; color: rgba(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="LC425" class="line" lang="c">    <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">indexLock</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">},</span> <span class="n" style="color: #333;">cciLock</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">index_ptr</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC427" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="c">    </span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">key</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="LC430" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* likely undefined region */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="457" style="width: 35px; color: rgba(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="457" style="width: 35px; color: rgba(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">@@ -457,7 +457,7 @@ void hashMapCCI_add_thread(HashMapCCI *dest, long unsigned key, int newpos, unsi</td>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="c"><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">hashMapCCI_load</span><span class="p">(</span><span class="n" style="color: #333;">HashMapCCI</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="c">    </span>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC460" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff right"> </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="LC460" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">long</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="LC461" class="line" lang="c">    </span>

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<pre style="margin: 0;"> <span id="LC462" 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="LC463" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">src</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="469" style="width: 35px; color: rgba(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="469" style="width: 35px; color: rgba(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">@@ -469,7 +469,15 @@ HashMapCCI * hashMapCCI_load(HashMapCCI *src, int seq, int len, int kmersize) {</td>

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="c">    </span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* get seq */</span></span>

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<pre style="margin: 0;">-<span id="LC472" class="line" lang="c">    <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="p">((</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="c">    <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC473" 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="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">src</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;">size</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</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>

</pre>

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<pre style="margin: 0;">+<span id="LC475" 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;">"Corrupted *.seq.b</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC476" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="c">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="478" 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="LC478" class="line" lang="c">                    <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC480" class="line" lang="c">    <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="481" style="width: 35px; color: rgba(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="LC481" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="482" style="width: 35px; color: rgba(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="LC482" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* add k-mers */</span></span>

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="c">    <span class="n" style="color: #333;">shifter</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmerindex</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="486" style="width: 35px; color: rgba(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="494" style="width: 35px; color: rgba(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">@@ -486,6 +494,7 @@ HashMapCCI * hashMapCCI_load_thread(HashMapCCI *src, int seq, int len, int kmers</td>

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="c">    <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lock</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">},</span> <span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thread_wait</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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<pre style="margin: 0;"> <span id="LC495" class="line" lang="c">    <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="496" style="width: 35px; color: rgba(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="LC496" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">,</span> <span class="n" style="color: #333;">chunk</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">check</span><span class="p">;</span></span>

</pre>

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489

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498

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

490

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<td class="diff-line-num new_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* init */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

491

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<td class="diff-line-num new_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

500

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<pre style="margin: 0;"> <span id="LC500" class="line" lang="c">    <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="496" style="width: 35px; color: rgba(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="505" style="width: 35px; color: rgba(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">@@ -496,7 +505,15 @@ HashMapCCI * hashMapCCI_load_thread(HashMapCCI *src, int seq, int len, int kmers</td>

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496

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<td class="diff-line-num new_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

505

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="c">            <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

506

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

498

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<td class="diff-line-num new_line" data-linenumber="507" style="width: 35px; color: rgba(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="LC507" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* get seq */</span></span>

</pre>

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499

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<td class="diff-line-num new_line old" data-linenumber="508" style="width: 35px; color: rgba(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="LC499" class="line" lang="c">            <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="p">((</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="508" 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="LC508" class="line" lang="c">            <span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="509" 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">

509

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">src</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;">check</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="510" 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">

510

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">check</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="511" 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">

511

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="c">                            <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="512" 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">

512

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="c">                    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="500" 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="diff-line-num new new_line" data-linenumber="513" 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">

513

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<pre style="margin: 0;">+<span id="LC513" 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;">"Corrupted *.seq.b</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="514" 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="LC514" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="515" 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">

515

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="516" 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="LC516" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC517" 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="LC518" class="line" lang="c">            <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="519" style="width: 35px; color: rgba(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="LC519" class="line" lang="c">    <span class="p">}</span></span>

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</li>

<li id="fe684ebf71f22762560b62973b5be5098b7ce2a4">

<a href="https://salsa.debian.org/med-team/kma/-/commit/c5c372bbfad911d7fe80e3aa1645d2e2572f6fdc#fe684ebf71f22762560b62973b5be5098b7ce2a4"><strong>hashmapcci.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,9 +23,9 @@</td>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef HASHMAPCCI</span></span>

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<pre style="margin: 0;"> <span id="LC24" 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;">hashMapCCI</span> <span class="n" style="color: #333;">HashMapCCI</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">hashMapCCI</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">mask</span><span class="p">;</span></span>

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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">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">mask</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// seqlen</span></span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// size of index</span></span>

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<td class="diff-line-num new old_line" data-linenumber="29" 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="LC28" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </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 class="c1" style="color: #998; font-style: italic;">// size of index</span></span>

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<td class="diff-line-num old_line" 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="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">kmerindex</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC30" 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;">index</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// k-mer posititions in seq / chain</span></span>

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<pre style="margin: 0;"> <span id="LC31" 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;">chain</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// k-mer collision positions</span></span>

</pre>

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<br>

</li>

<li id="ca9efd475143efe0a1b0464c67f49900d98ca75a">

<a href="https://salsa.debian.org/med-team/kma/-/commit/c5c372bbfad911d7fe80e3aa1645d2e2572f6fdc#ca9efd475143efe0a1b0464c67f49900d98ca75a"><strong>runkma.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1396" style="width: 35px; color: rgba(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="1396" style="width: 35px; color: rgba(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">@@ -1396,6 +1396,9 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>

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<pre style="margin: 0;"> <span id="LC1396" class="line" lang="c">   <span class="n" style="color: #333;">seqin_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ftell</span><span class="p">(</span><span class="n" style="color: #333;">seq_in</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC1397" class="line" lang="c">   <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC1398" class="line" lang="c">   <span class="n" style="color: #333;">seq_in_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileno</span><span class="p">(</span><span class="n" style="color: #333;">seq_in</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1399" 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="diff-line-num new new_line" data-linenumber="1399" 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">

1399

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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">lseek</span><span class="p">(</span><span class="n" style="color: #333;">seq_in_no</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1399" 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="diff-line-num new new_line" data-linenumber="1400" 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">

1400

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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="c">           <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1399" 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="diff-line-num new new_line" data-linenumber="1401" 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">

1401

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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1399

</td>

<td class="diff-line-num new_line" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1402

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<pre style="margin: 0;"> <span id="LC1402" class="line" lang="c">   <span class="n" style="color: #333;">templatefilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1400

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<td class="diff-line-num new_line" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1403

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<pre style="margin: 0;"> <span id="LC1403" class="line" lang="c">   </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1401

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<td class="diff-line-num new_line" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1404

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<pre style="margin: 0;"> <span id="LC1404" class="line" lang="c">   <span class="cm" style="color: #998; font-style: italic;">/* allocate stuff */</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2228" style="width: 35px; color: rgba(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="2231" style="width: 35px; color: rgba(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">@@ -2228,7 +2231,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>

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<td class="diff-line-num old_line" data-linenumber="2228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2228

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<td class="diff-line-num new_line" data-linenumber="2231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2231

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<pre style="margin: 0;"> <span id="LC2231" 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;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2229

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<td class="diff-line-num new_line" data-linenumber="2232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2232

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<pre style="margin: 0;"> <span id="LC2232" 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;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2230

</td>

<td class="diff-line-num new_line" data-linenumber="2233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2233

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<pre style="margin: 0;"> <span id="LC2233" 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;">ef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="2231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2231

</td>

<td class="diff-line-num new_line old" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC2231" class="line" lang="c">           <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">fileno</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq_in</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2232" 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="diff-line-num new new_line" data-linenumber="2234" 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">

2234

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<pre style="margin: 0;">+<span id="LC2234" class="line" lang="c">           <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">seq_in_no</span></span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2232

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<td class="diff-line-num new_line" data-linenumber="2235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2235

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<pre style="margin: 0;"> <span id="LC2235" 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;">kmersize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2233

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<td class="diff-line-num new_line" data-linenumber="2236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2236

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<pre style="margin: 0;"> <span id="LC2236" class="line" lang="c">           <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2234

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<td class="diff-line-num new_line" data-linenumber="2237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2237

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

<pre style="margin: 0;"> <span id="LC2237" 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;">file_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileCount</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2292" style="width: 35px; color: rgba(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="2295" style="width: 35px; color: rgba(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">@@ -2292,7 +2295,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>

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<td class="diff-line-num old_line" data-linenumber="2292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2292

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<td class="diff-line-num new_line" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2295

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

<pre style="margin: 0;"> <span id="LC2295" 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;">bcd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2293

</td>

<td class="diff-line-num new_line" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2296

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<pre style="margin: 0;"> <span id="LC2296" 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;">sam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2294

</td>

<td class="diff-line-num new_line" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2297

</td>

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

<pre style="margin: 0;"> <span id="LC2297" 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;">ef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2295

</td>

<td class="diff-line-num new_line old" data-linenumber="2298" style="width: 35px; color: rgba(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="LC2295" class="line" lang="c">   <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">fileno</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq_in</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2296" 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="diff-line-num new new_line" data-linenumber="2298" 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">

2298

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<pre style="margin: 0;">+<span id="LC2298" class="line" lang="c">   <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">seq_in_no</span></span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2296

</td>

<td class="diff-line-num new_line" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2299

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<pre style="margin: 0;"> <span id="LC2299" 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;">kmersize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmersize</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2297

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<td class="diff-line-num new_line" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2300

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<pre style="margin: 0;"> <span id="LC2300" class="line" lang="c">   <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2298

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<td class="diff-line-num new_line" data-linenumber="2301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2301

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<pre style="margin: 0;"> <span id="LC2301" 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;">file_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileCount</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2329" style="width: 35px; color: rgba(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="2332" style="width: 35px; color: rgba(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">@@ -2329,7 +2332,6 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>

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<td class="diff-line-num old_line" data-linenumber="2329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2329

</td>

<td class="diff-line-num new_line" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2332

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<pre style="margin: 0;"> <span id="LC2332" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2330

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<td class="diff-line-num new_line" data-linenumber="2333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2333

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<pre style="margin: 0;"> <span id="LC2333" 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;">"# Template</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Progress</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2331

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<td class="diff-line-num new_line" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2334

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<pre style="margin: 0;"> <span id="LC2334" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2332

</td>

<td class="diff-line-num new_line old" data-linenumber="2335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC2332" class="line" lang="c">   </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2333

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<td class="diff-line-num new_line" data-linenumber="2335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2335

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<pre style="margin: 0;"> <span id="LC2335" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">DB_size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">template</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2334

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<td class="diff-line-num new_line" data-linenumber="2336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2336

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<pre style="margin: 0;"> <span id="LC2336" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2335

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<td class="diff-line-num new_line" data-linenumber="2337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2337

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<pre style="margin: 0;"> <span id="LC2337" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">progress</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="f80652dda49a7117428c0f92935664fc8cd4e2d1">

<a href="https://salsa.debian.org/med-team/kma/-/commit/c5c372bbfad911d7fe80e3aa1645d2e2572f6fdc#f80652dda49a7117428c0f92935664fc8cd4e2d1"><strong>spltdb.c</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="1541" style="width: 35px; color: rgba(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="1541" style="width: 35px; color: rgba(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">@@ -1541,6 +1541,9 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>

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<td class="diff-line-num old_line" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1541

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<td class="diff-line-num new_line" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1541

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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="c">   <span class="n" style="color: #333;">seqin_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ftell</span><span class="p">(</span><span class="n" style="color: #333;">seq_in</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1542

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<td class="diff-line-num new_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1542

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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="c">   <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">seq_in</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1543

</td>

<td class="diff-line-num new_line" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1543

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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="c">   <span class="n" style="color: #333;">seq_in_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileno</span><span class="p">(</span><span class="n" style="color: #333;">seq_in</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="1544" 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="diff-line-num new new_line" data-linenumber="1544" 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">

1544

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1544" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">lseek</span><span class="p">(</span><span class="n" style="color: #333;">seq_in_no</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1544" 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="diff-line-num new new_line" data-linenumber="1545" 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">

1545

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1545" class="line" lang="c">           <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1544" 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="diff-line-num new new_line" data-linenumber="1546" 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">

1546

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1546" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1544

</td>

<td class="diff-line-num new_line" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1547

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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="c">   <span class="n" style="color: #333;">templatefilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1545

</td>

<td class="diff-line-num new_line" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1548

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<pre style="margin: 0;"> <span id="LC1548" class="line" lang="c">   <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".name"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1546

</td>

<td class="diff-line-num new_line" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1549

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<pre style="margin: 0;"> <span id="LC1549" class="line" lang="c">   <span class="n" style="color: #333;">name_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>

</pre>

</td>

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</table>

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</li>

<li id="2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">

<a href="https://salsa.debian.org/med-team/kma/-/commit/c5c372bbfad911d7fe80e3aa1645d2e2572f6fdc#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">

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

<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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<td class="diff-line-num 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">

17

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<td class="diff-line-num 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">

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>

</td>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

</td>

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<td class="diff-line-num old_line" 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

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

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<td class="diff-line-num new_line 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.<span class="idiff left right">6</span>"</span></span></pre>

</td>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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.<span class="idiff left right">7</span>"</span></span></pre>

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