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<h3>
Steffen Möller 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/694b4807c99bddd1372450e2a4ecc175f482e50f">694b4807</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-07-13T23:54:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.2</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1fa9be53365c168355414c67a78869ee9befb877">
dist.c
</a>
</li>
<li class="file-stats">
<a href="#a9c0f53d72073d487e5f909ae155567290a2a5fa">
dist.h
</a>
</li>
<li class="file-stats">
<a href="#4a59da3f123fbc2eabd4b7c4d9c4e2f54d6af662">
kmers.c
</a>
</li>
<li class="file-stats">
<a href="#43638494320234f912fa37977d784743664b2c37">
matrix.c
</a>
</li>
<li class="file-stats">
<a href="#3f89f8a0bdf3802e22af73d583945fa953dd966b">
matrix.h
</a>
</li>
<li class="file-stats">
<a href="#ca9efd475143efe0a1b0464c67f49900d98ca75a">
runkma.c
</a>
</li>
<li class="file-stats">
<a href="#f9ead8e7fb7b1680f786604627e0ac2147f4b7ef">
savekmers.c
</a>
</li>
<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="1fa9be53365c168355414c67a78869ee9befb877">
<a href="https://salsa.debian.org/med-team/kma/-/commit/694b4807c99bddd1372450e2a4ecc175f482e50f#1fa9be53365c168355414c67a78869ee9befb877"><strong>dist.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,10 +22,15 @@</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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<td class="diff-line-num 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">
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<td class="diff-line-num 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/mman.h></span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/param.h></span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "dist.h"</span></span>
</pre>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "hashmapkma.h"</span></span>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "matrix.h"</span></span>
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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
27
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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "pherror.h"</span></span>
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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "runkma.h"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "threader.h"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="33" 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="LC33" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "tmp.h"</span></span>
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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(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="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define missArg(opt) fprintf(stderr, "Missing argument at %s.\n", opt); exit(1);</span></span>
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30
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define invaArg(opt) fprintf(stderr, "Invalid value parsed at %s.\n", opt); exit(1);</span></span>
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31
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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" style="width: 35px; color: rgba(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="116" style="width: 35px; color: rgba(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">@@ -111,7 +116,6 @@ HashMapKMA * loadValues(const char *filename) {</td>
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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
111
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<td class="diff-line-num new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
112
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<td class="diff-line-num new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
113
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<td class="diff-line-num new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">values</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(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="LC114" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">shmFlag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(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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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> </span>
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116
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check for megaMap */</span></span>
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117
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exist</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="147" style="width: 35px; color: rgba(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="151" style="width: 35px; color: rgba(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">@@ -147,7 +151,6 @@ HashMapKMA * loadValues(const char *filename) {</td>
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147
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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148
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> <span class="p">}</span></span>
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149
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exist_l</span> <span class="o" style="font-weight: 600;">=</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="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value_index</span><span class="p">);</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">shmFlag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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151
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"> </span>
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152
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">);</span></span>
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153
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dest</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="162" style="width: 35px; color: rgba(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="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -162,7 +165,7 @@ void destroyValues(HashMapKMA *src) {</td>
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162
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"></span>
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163
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerSimilarity</span><span class="p">(</span><span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">DB</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">)</span> <span class="p">{</span></span>
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">el</span><span class="p">,</span> <span class="n" style="color: #333;">vs</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">**</span></span><span class="n" style="color: #333;"><span class="idiff right">D</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">el</span><span class="p">,</span> <span class="n" style="color: #333;">vs</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">v_i</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">D</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">Di</span></span><span class="p">;</span></span>
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166
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exist</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_j</span><span class="p">;</span></span>
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167
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170
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<pre style="margin: 0;"> <span id="LC170" 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;">n</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exist_l</span><span class="p">;</span></span>
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168
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_si</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_sj</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="186" style="width: 35px; color: rgba(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="189" style="width: 35px; color: rgba(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">@@ -186,10 +189,12 @@ void kmerSimilarity(HashMapKMA *DB, Matrix *Dist, int *N) {</td>
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186
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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187
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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188
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="c"> <span class="n" style="color: #333;">values_sj</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">values_si</span><span class="p">;</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"> <span class="n" style="color: #333;">v_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_si</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"> <span class="n" style="color: #333;">Di</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">D</span><span class="p">[</span><span class="n" style="color: #333;">v_i</span><span class="p">];</span></span>
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189
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">D</span><span class="p"><span class="idiff left">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">values_si</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>[</span><span class="o" style="font-weight: 600;">*--</span><span class="n" style="color: #333;">values_sj</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">D<span class="idiff left right">i</span></span><span class="p">[</span><span class="o" style="font-weight: 600;">*--</span><span class="n" style="color: #333;">values_sj</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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191
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="c"> <span class="p">}</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">values_si</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">];</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">v_i</span></span><span class="p">];</span></span>
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193
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"> <span class="p">}</span></span>
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194
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199
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<pre style="margin: 0;"> <span id="LC199" 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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195
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">values_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">values</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="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>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -198,10 +203,12 @@ void kmerSimilarity(HashMapKMA *DB, Matrix *Dist, int *N) {</td>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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199
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <span class="n" style="color: #333;">values_j</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">values_i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="c"> <span class="n" style="color: #333;">v_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c"> <span class="n" style="color: #333;">Di</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">D</span><span class="p">[</span><span class="n" style="color: #333;">v_i</span><span class="p">];</span></span>
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">D</span><span class="p"><span class="idiff left">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">values_i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>[</span><span class="o" style="font-weight: 600;">*--</span><span class="n" style="color: #333;">values_j</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">D<span class="idiff left right">i</span></span><span class="p">[</span><span class="o" style="font-weight: 600;">*--</span><span class="n" style="color: #333;">values_j</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">values_i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">v_i</span></span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -209,192 +216,555 @@ void kmerSimilarity(HashMapKMA *DB, Matrix *Dist, int *N) {</td>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="c"> <span class="n" style="color: #333;">destroyValues</span><span class="p">(</span><span class="n" style="color: #333;">DB</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmer<span class="idiff left">Dist</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">FILE</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Matrix</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">Dist</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">N</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">FILE</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">name_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Qseqs</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">template_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">format</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmer<span class="idiff left">Similarity_thread</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">HashMapKMA</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">DB</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Matrix</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">Dist</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">N</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">thread_num</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">volatile</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">lock</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">D</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" 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;">thread_wait</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" 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;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" 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;">n</span><span class="p">;</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">el</span><span class="p">,</span> <span class="n" style="color: #333;">vs</span><span class="p">,</span> <span class="n" style="color: #333;">v_i</span><span class="p">,</span> <span class="n" style="color: #333;">chunk</span><span class="p">,</span> <span class="n" style="color: #333;">chunkster</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">D</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Di</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dptr</span><span class="p">;</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exist</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_j</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="229" 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">
229
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<pre style="margin: 0;">+<span id="LC229" 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;">pos</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;">exist_l</span><span class="p">;</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_si</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_sj</span><span class="p">;</span></span>
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218
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c"> </span>
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219
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* init */</span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="c"> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="c"> </span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"k-mer distance"</span><span class="p">);</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="c"> <span class="n" style="color: #333;">el</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v_index</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">UINT_MAX</span><span class="p">;</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="c"> <span class="n" style="color: #333;">vs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">USHRT_MAX</span><span class="p">;</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="c"> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">;</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="c"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" 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;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* static init */</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" 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>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">thread_wait</span><span class="p">)</span> <span class="p">{</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_num</span><span class="p">;</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c"> <span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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224
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> <span class="p">}</span></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
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228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" 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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231
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10.10s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="c"> </span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get values */</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">chunk</span><span class="p">)</span> <span class="p">{</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get next chunk */</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" 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>
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253
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<pre style="margin: 0;">+<span id="LC253" 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;">next</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="254" 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">
254
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<pre style="margin: 0;">+<span id="LC254" 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="p">(</span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">chunk</span><span class="p">))</span> <span class="p">{</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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232
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">+<span id="LC257" 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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233
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<td class="diff-line-num new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="c"> </span>
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234
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<td class="diff-line-num new_line old" data-linenumber="259" style="width: 35px; color: rgba(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="LC234" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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235
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<td class="diff-line-num new_line old" data-linenumber="259" style="width: 35px; color: rgba(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="LC235" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d"</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update chunk */</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="c"> <span class="n" style="color: #333;">exist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exist</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="c"> <span class="n" style="color: #333;">exist_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exist_l</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" 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">
262
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<pre style="margin: 0;">+<span id="LC262" 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;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chunk</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="c"> <span class="n" style="color: #333;">chunkster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" 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">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="c"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;">+<span id="LC265" 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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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">chunkster</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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236
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> <span class="p">}</span></span>
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237
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="238" 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="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">chunkster</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" 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">
269
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<pre style="margin: 0;">+<span id="LC269" 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;">el</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">exist</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">exist_l</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">vs</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="c"> <span class="n" style="color: #333;">values_si</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_si</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="c"> <span class="n" style="color: #333;">values_si</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="275" 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">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="277" 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">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="c"> <span class="n" style="color: #333;">values_sj</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">values_si</span><span class="p">;</span></span>
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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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c"> <span class="n" style="color: #333;">v_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_si</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num 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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="c"> <span class="n" style="color: #333;">Di</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">D</span><span class="p">[</span><span class="n" style="color: #333;">v_i</span><span class="p">];</span></span>
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<td class="diff-line-num new new_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">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="c"> <span class="n" style="color: #333;">Dptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Di</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*--</span><span class="n" style="color: #333;">values_sj</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="282" 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">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="c"> <span class="n" style="color: #333;">__sync_add_and_fetch</span><span class="p">(</span><span class="n" style="color: #333;">Dptr</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" 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">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="c"> <span class="n" style="color: #333;">Dptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">v_i</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="285" 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">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">__sync_add_and_fetch</span><span class="p">(</span><span class="n" style="color: #333;">Dptr</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" 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">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="288" 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">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="c"> <span class="n" style="color: #333;">values_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">values</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 new new_line" data-linenumber="289" 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">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" 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">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="c"> <span class="n" style="color: #333;">values_i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="292" 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">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="c"> <span class="n" style="color: #333;">values_j</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">values_i</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="294" 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">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">v_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="295" 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">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="c"> <span class="n" style="color: #333;">Di</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">D</span><span class="p">[</span><span class="n" style="color: #333;">v_i</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="296" 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">
296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c"> <span class="n" style="color: #333;">Dptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Di</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*--</span><span class="n" style="color: #333;">values_j</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="298" 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">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="c"> <span class="n" style="color: #333;">__sync_add_and_fetch</span><span class="p">(</span><span class="n" style="color: #333;">Dptr</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="c"> <span class="p">}</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="c"> <span class="n" style="color: #333;">Dptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">v_i</span><span class="p">;</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c"> <span class="n" style="color: #333;">__sync_add_and_fetch</span><span class="p">(</span><span class="n" style="color: #333;">Dptr</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="c"> <span class="p">}</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="c"> <span class="p">}</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="c"> <span class="n" style="color: #333;">__sync_sub_and_fetch</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="c"> <span class="p">}</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="c"> <span class="p">}</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="c"> <span class="p">}</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="309" 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">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">__sync_sub_and_fetch</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_wait</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="310" 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">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="c"> <span class="n" style="color: #333;">wait_atomic</span><span class="p">(</span><span class="n" style="color: #333;">thread_wait</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="311" 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">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="312" 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">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c"> <span class="n" style="color: #333;">destroyValues</span><span class="p">(</span><span class="n" style="color: #333;">DB</span><span class="p">);</span></span>
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238
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">name_file</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="LC314" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerShared</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">kmerDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Nj</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="c"><span class="p">}</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="c"></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">kmerShared</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">D</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="c"></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">chi2dist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="c"> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Nj</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Nj</span><span class="p">);</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="c"><span class="p">}</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printIntLtdPhy</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">method</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">distPtr</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">D</span><span class="p">;</span></span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" 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;">thread_wait1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">thread_wait2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">next_i</span><span class="p">,</span> <span class="n" style="color: #333;">next_j</span><span class="p">,</span> <span class="n" style="color: #333;">entrance</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" 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;">row_bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="c"> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thread_wait</span><span class="p">;</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">j_end</span><span class="p">,</span> <span class="n" style="color: #333;">chunk</span><span class="p">,</span> <span class="n" style="color: #333;">N_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">D</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Di</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile_chunk</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC338" 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="LC248" class="line" lang="c"> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"shared k-mers"</span><span class="p">);</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="c"> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">;</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1048576</span><span class="p">;</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" 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>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">row_bias</span><span class="p">)</span> <span class="p">{</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="344" 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">
344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %-35s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="p">);</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="346" 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">
346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row_bias</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10d"</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="c"> <span class="n" style="color: #333;">next_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="c"> <span class="n" style="color: #333;">next_j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">entrance</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_num</span><span class="p">;</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_wait1</span><span class="p">;</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" 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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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_num</span><span class="p">;</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_wait2</span><span class="p">;</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="c"> <span class="p">}</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">entrance</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_wait1</span><span class="p">;</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" 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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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_wait2</span><span class="p">;</span></span>
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252
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="c"> <span class="p">}</span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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257
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<td class="diff-line-num new_line old" data-linenumber="361" style="width: 35px; color: rgba(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="LC257" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" 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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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="363" 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">
363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">next_i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" 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>
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<td class="diff-line-num new new_line" data-linenumber="365" 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">
365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check for new row */</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">next_i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">next_j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="367" 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">
367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">next_i</span><span class="p">;</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="c"> <span class="p">}</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="372" 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">
372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="c"> <span class="n" style="color: #333;">next_j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="373" 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">
373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">next_i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="374" 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">
374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="c"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="376" 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">
376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row_bias</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="377" 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">
377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="378" 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">
378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row_bias</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%-10.10s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="379" 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">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="380" 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">
380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="381" 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">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="c"> <span class="n" style="color: #333;">outfile</span><span class="p">[</span><span class="n" style="color: #333;">row_bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" 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">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">row_bias</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="383" 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">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="c"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="384" 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">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="c"> <span class="p">}</span></span>
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258
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<td class="diff-line-num new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
385
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<pre style="margin: 0;"> <span id="LC385" 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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259
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<td class="diff-line-num new_line old" data-linenumber="386" style="width: 35px; color: rgba(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="LC259" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10.10s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="386" 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">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_i</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="387" 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">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_j</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="388" 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">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="c"> <span class="n" style="color: #333;">next_j</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">chunk</span><span class="p">;</span></span>
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260
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="c"> <span class="p">}</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="c"> <span class="n" style="color: #333;">outfile_chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="391" 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">
391
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<pre style="margin: 0;">+<span id="LC391" 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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261
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<td class="diff-line-num new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="c"> </span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="393" 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">
393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">chunk</span><span class="p">)</span> <span class="p">{</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="c"> <span class="n" style="color: #333;">N_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="395" 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">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="c"> <span class="n" style="color: #333;">j_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chunk</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chunk</span><span class="p">);</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="c"> <span class="n" style="color: #333;">Di</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">D</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="c"> <span class="n" style="color: #333;">Nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="398" 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">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j_end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="c"> <span class="n" style="color: #333;">outfile_chunk</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile_chunk</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%10d"</span><span class="p">,</span> <span class="n" style="color: #333;">distPtr</span><span class="p">(</span><span class="n" style="color: #333;">N_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Di</span><span class="p">));</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="401" 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">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* fix null character */</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile_chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;">:</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>
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264
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="c"> <span class="p">}</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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266
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="c"> <span class="p">}</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">name_file</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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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="406" 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">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* wait for matrix to finish */</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" 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>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">--*</span><span class="n" style="color: #333;">thread_wait</span><span class="p">)</span> <span class="p">{</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" 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 new_line" data-linenumber="410" 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">
410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="c"> <span class="n" style="color: #333;">wait_atomic</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thread_wait</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="411" 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">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="412" 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">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">name_file</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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<td class="diff-line-num new new_line" data-linenumber="413" 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">
413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="414" 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">
414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerQuery</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Ni</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="c"><span class="p">}</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="c"></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerTemplate</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Nj</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerQuery</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">)</span> <span class="p">{</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerAvg</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">200</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;">D</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Nj</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="c"><span class="p">}</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerInvAvg</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">200</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;">D</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Nj</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerJaccardDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Nj</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerJaccardSim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Nj</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerCosineDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Nj</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerCosineSim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Nj</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerOverlapCoef</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Nj</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Nj</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerInvOverlapCoef</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Nj</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">Ni</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Nj</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="c"><span class="p">}</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printDoublePhy</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">formatString</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ltd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">method</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">distPtr</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">D</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC460" 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;">thread_wait1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">thread_wait2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">next_i</span><span class="p">,</span> <span class="n" style="color: #333;">next_j</span><span class="p">,</span> <span class="n" style="color: #333;">entrance</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" 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;">row_bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="c"> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thread_wait</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">j_end</span><span class="p">,</span> <span class="n" style="color: #333;">chunk</span><span class="p">,</span> <span class="n" style="color: #333;">N_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">D</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Di</span><span class="p">;</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">endChar</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile_chunk</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC467" 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="LC468" class="line" lang="c"> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Query k-mer coverage"</span><span class="p">);</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="c"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1048576</span><span class="p">;</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" 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>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">row_bias</span><span class="p">)</span> <span class="p">{</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %-35s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="p">);</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="c"> <span class="p">}</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row_bias</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10d"</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="c"> <span class="n" style="color: #333;">next_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="c"> <span class="n" style="color: #333;">next_j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">entrance</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_num</span><span class="p">;</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_wait1</span><span class="p">;</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" 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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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_num</span><span class="p">;</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_wait2</span><span class="p">;</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="c"> <span class="p">}</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">entrance</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_wait1</span><span class="p">;</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" 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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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="c"> <span class="n" style="color: #333;">thread_wait</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_wait2</span><span class="p">;</span></span>
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281
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="c"> <span class="p">}</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" 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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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="c"> </span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">next_i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" 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>
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<td class="diff-line-num new new_line" data-linenumber="494" 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">
494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check for new row */</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">ltd</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">next_i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">next_j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">next_j</span><span class="p">))</span> <span class="p">{</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">next_i</span><span class="p">;</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="498" 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">
498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">ltd</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="c"> <span class="p">}</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="c"> <span class="n" style="color: #333;">next_j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span><span class="p">;</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">next_i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="c"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row_bias</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="506" 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">
506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="507" 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">
507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row_bias</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%-10.10s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="c"> <span class="p">}</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" 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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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="c"> <span class="n" style="color: #333;">outfile</span><span class="p">[</span><span class="n" style="color: #333;">row_bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">row_bias</span><span class="p">;</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="c"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="c"> <span class="p">}</span></span>
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287
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514
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<pre style="margin: 0;"> <span id="LC514" 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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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10.10s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_i</span><span class="p">;</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_j</span><span class="p">;</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="c"> <span class="n" style="color: #333;">next_j</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">chunk</span><span class="p">;</span></span>
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289
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="c"> <span class="p">}</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="c"> <span class="n" style="color: #333;">outfile_chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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290
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="c"> </span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.2f"</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">chunk</span><span class="p">)</span> <span class="p">{</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ltd</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="c"> <span class="n" style="color: #333;">j_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chunk</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chunk</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="c"> <span class="n" style="color: #333;">endChar</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">j_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;">:</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>
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294
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">d</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">D</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">D</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">fprintf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%.2f"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">N</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">])</span>;</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">j_end</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Dist</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">n</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chunk</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Dist</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">n</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chunk</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">endChar</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">j_end</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Dist</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">n</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'\n'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff right">'\t'</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="c"> <span class="p">}</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="c"> <span class="n" style="color: #333;">N_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="c"> <span class="n" style="color: #333;">Di</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">D</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="c"> <span class="n" style="color: #333;">Nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j_end</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j_end</span><span class="p">)</span> <span class="p">{</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="c"> <span class="n" style="color: #333;">outfile_chunk</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile_chunk</span><span class="p">,</span> <span class="n" style="color: #333;">formatString</span><span class="p">,</span> <span class="n" style="color: #333;">distPtr</span><span class="p">(</span><span class="n" style="color: #333;">N_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Di</span><span class="p">));</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="c"> <span class="p">}</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j_end</span><span class="p">)</span> <span class="p">{</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="c"> <span class="n" style="color: #333;">outfile_chunk</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile_chunk</span><span class="p">,</span> <span class="n" style="color: #333;">formatString</span><span class="p">,</span> <span class="n" style="color: #333;">distPtr</span><span class="p">(</span><span class="n" style="color: #333;">N_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="n" style="color: #333;">D</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="c"> <span class="p">}</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j_end</span><span class="p">)</span> <span class="p">{</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="c"> <span class="n" style="color: #333;">outfile_chunk</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile_chunk</span><span class="p">,</span> <span class="n" style="color: #333;">formatString</span><span class="p">,</span> <span class="n" style="color: #333;">distPtr</span><span class="p">(</span><span class="n" style="color: #333;">N_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Di</span><span class="p">));</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="c"> <span class="n" style="color: #333;">outfile_chunk</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile_chunk</span><span class="p">,</span> <span class="n" style="color: #333;">formatString</span><span class="p">,</span> <span class="n" style="color: #333;">distPtr</span><span class="p">(</span><span class="n" style="color: #333;">N_i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="n" style="color: #333;">D</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" 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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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="c"> <span class="n" style="color: #333;">outfile_chunk</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile_chunk</span><span class="p">,</span> <span class="n" style="color: #333;">formatString</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Nj</span><span class="p">;</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="c"> <span class="p">}</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="c"> <span class="p">}</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* fix null character */</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile_chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endChar</span><span class="p">;</span></span>
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298
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="c"> <span class="p">}</span></span>
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299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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300
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c"> <span class="p">}</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">name_file</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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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="c"> </span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* wait for matrix to finish */</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" 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>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">--*</span><span class="n" style="color: #333;">thread_wait</span><span class="p">)</span> <span class="p">{</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="c"> <span class="n" style="color: #333;">wait_atomic</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thread_wait</span><span class="p">);</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" 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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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">name_file</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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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="c"> <span class="n" style="color: #333;">row_bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" 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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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="c"> <span class="p">}</span></span>
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302
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="c"><span class="p">}</span></span>
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303
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="c"></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerTemplate</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">)</span> <span class="p">{</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="c"> </span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">D</span><span class="p">;</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">getPhySize</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</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;">n</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ltdMat</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">covMat</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">)</span> <span class="p">{</span></span>
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309
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="c"> </span>
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310
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<td class="diff-line-num new_line old" data-linenumber="573" style="width: 35px; color: rgba(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="cm" style="color: #998; font-style: italic;">/* init */</span></span>
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311
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<td class="diff-line-num new_line old" data-linenumber="573" style="width: 35px; color: rgba(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="LC311" class="line" lang="c"> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">;</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="c"> <span class="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>
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312
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574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="c"> </span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get name name */</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="577" 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">
577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_END</span><span class="p">);</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="c"> <span class="n" style="color: #333;">size</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;">name_file</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="579" 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">
579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="c"> <span class="n" style="color: #333;">rewind</span><span class="p">(</span><span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="580" 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">
580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="581" 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">
581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="c"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="c"> <span class="p">}</span></span>
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313
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">fprintf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"#%s</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Template k-mer coverage"</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">38</span></span><span class="p">;</span></span>
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315
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585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="c"> <span class="p">}</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="c"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
321
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<td class="diff-line-num new_line old" data-linenumber="586" style="width: 35px; color: rgba(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="LC321" 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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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10.10s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="c"> <span class="p">}</span></span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="c"> </span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.2f"</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
328
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<td class="diff-line-num new_line old" data-linenumber="586" style="width: 35px; color: rgba(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="LC328" 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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329
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<td class="diff-line-num new_line old" data-linenumber="586" style="width: 35px; color: rgba(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="LC329" class="line" lang="c"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">D</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">D</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.2f"</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="c"> <span class="p">}</span></span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="c"> <span class="p">}</span></span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="c"> </span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* phy size */</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="c"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="c"> </span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* ltd cell size */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="591" 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">
591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ltdMat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(((</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="c"> </span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* cov cell size */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="594" 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">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">covMat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="c"> </span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get number of matrices to make */</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="c"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="c"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">covMat</span><span class="p">;</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">^=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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334
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="c"> <span class="p">}</span></span>
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335
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">name_file</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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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="p">{</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="c"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">covMat</span><span class="p">;</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">^=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="c"> <span class="p">}</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">flag</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="c"> <span class="p">}</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="c"> </span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="c"><span class="p">}</span></span>
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">kmerAvg</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">FILE</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Matrix</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">Dist</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">N</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">FILE</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">name_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Qseqs</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">template_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">format</span></span><span class="p">)</span> <span class="p">{</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">mfile</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">FILE</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">size</span></span><span class="p">)</span> <span class="p">{</span></span>
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339
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616
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="c"> </span>
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340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">D</span><span class="p">;</span></span>
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341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfileM</span><span class="p">;</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="619" 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">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</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="n" style="color: #333;">putc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EOF</span><span class="p">)</span> <span class="p">{</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="622" 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">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="c"> <span class="n" style="color: #333;">rewind</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="623" 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">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mmap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">PROT_READ</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">PROT_WRITE</span><span class="p">,</span> <span class="n" style="color: #333;">MAP_SHARED</span><span class="p">,</span> <span class="n" style="color: #333;">fileno</span><span class="p">(</span><span class="n" style="color: #333;">outfile</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="LC624" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">MAP_FAILED</span><span class="p">)</span> <span class="p">{</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="c"> <span class="p">}</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="c"> <span class="n" style="color: #333;">posix_madvise</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">POSIX_MADV_SEQUENTIAL</span><span class="p">);</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="c"> </span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">outfileM</span><span class="p">;</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="c"><span class="p">}</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="c"></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">threadDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arg</span><span class="p">)</span> <span class="p">{</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="c"> </span>
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634
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<pre style="margin: 0;">+<span id="LC634" 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>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="c"> <span class="n" style="color: #333;">DistThread</span> <span class="o" style="font-weight: 600;">*</span><span class="kr" style="font-weight: 600;">thread</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">;</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">;</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" 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;">ltdMat</span><span class="p">,</span> <span class="n" style="color: #333;">covMat</span><span class="p">;</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfileM</span><span class="p">;</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">;</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="c"> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">DB</span><span class="p">;</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="c"> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">;</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="c"> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">;</span></span>
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342
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643
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="c"> </span>
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343
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644
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* init */</span></span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="c"> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="c"> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">format</span><span class="p">;</span></span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="c"> <span class="n" style="color: #333;">thread_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_num</span><span class="p">;</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="c"> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">;</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="c"> <span class="n" style="color: #333;">ltdMat</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="c"> <span class="n" style="color: #333;">covMat</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">covMat</span><span class="p">;</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outfileM</span><span class="p">;</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="c"> <span class="n" style="color: #333;">name_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name_file</span><span class="p">;</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="c"> <span class="n" style="color: #333;">DB</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB</span><span class="p">;</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="c"> <span class="n" style="color: #333;">Dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Dist</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="c"> <span class="n" style="color: #333;">template_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Avg. k-mer coverage"</span><span class="p">);</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get kmer similarities and lengths */</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">thread_num</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="c"> <span class="n" style="color: #333;">kmerSimilarity_thread</span><span class="p">(</span><span class="n" style="color: #333;">DB</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" 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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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="c"> <span class="n" style="color: #333;">kmerSimilarity</span><span class="p">(</span><span class="n" style="color: #333;">DB</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">);</span></span>
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348
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="c"> <span class="p">}</span></span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Dist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="c"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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353
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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354
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<pre style="margin: 0;">-<span id="LC354" 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="LC355" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10.10s"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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356
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="c"> <span class="p">}</span></span>
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357
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="c"> </span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.2f"</span><span class="p">,</span> <span class="mi" style="color: #099;">200</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]));</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* k-mer dist, lt */</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="c"> <span class="n" style="color: #333;">printIntLtdPhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"k-mer distance"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerDist</span><span class="p">);</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* k-mer shared, lt */</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="c"> <span class="n" style="color: #333;">printIntLtdPhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"shared k-mers"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerShared</span><span class="p">);</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="c"> <span class="p">}</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* query cov, asym */</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="c"> <span class="n" style="color: #333;">printDoublePhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%10.6f"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Query k-mer coverage [%]"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerQuery</span><span class="p">);</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">covMat</span><span class="p">;</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="c"> <span class="p">}</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* template cov, asym */</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="p">{</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="c"> <span class="n" style="color: #333;">printDoublePhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%10.6f"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Template k-mer coverage [%]"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerTemplate</span><span class="p">);</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">covMat</span><span class="p">;</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="c"> <span class="p">}</span></span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* avg. cov, lt */</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="p">{</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="c"> <span class="n" style="color: #333;">printDoublePhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%10.6f"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Avg. k-mer coverage [%]"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerAvg</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="c"> <span class="p">}</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* inv. avg. cov, lt */</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="p">{</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="c"> <span class="n" style="color: #333;">printDoublePhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%10.6f"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Inverse Avg. k-mer coverage"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerInvAvg</span><span class="p">);</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="c"> <span class="p">}</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Jaccard dist */</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span> <span class="p">{</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="c"> <span class="n" style="color: #333;">printDoublePhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.8f"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Jaccard Distance"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerJaccardDist</span><span class="p">);</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="c"> <span class="p">}</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="c"> </span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Jaccard similarity */</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">128</span><span class="p">)</span> <span class="p">{</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="c"> <span class="n" style="color: #333;">printDoublePhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.8f"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Jaccard Similarity"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerJaccardSim</span><span class="p">);</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="c"> <span class="p">}</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Cosine dist */</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">256</span><span class="p">)</span> <span class="p">{</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="c"> <span class="n" style="color: #333;">printDoublePhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.8f"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Cosine distance"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerCosineDist</span><span class="p">);</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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362
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">name_file</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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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="c"> </span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Cosine similarity */</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">512</span><span class="p">)</span> <span class="p">{</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="c"> <span class="n" style="color: #333;">printDoublePhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.8f"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Cosine similarity"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerCosineSim</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="c"> <span class="p">}</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Szymkiewicz–Simpson similarity */</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="p">{</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="c"> <span class="n" style="color: #333;">printDoublePhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.8f"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Szymkiewicz–Simpson similarity"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerOverlapCoef</span><span class="p">);</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Szymkiewicz–Simpson dissimilarity */</span></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">2048</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="732" 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">
732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="c"> <span class="n" style="color: #333;">printDoublePhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.8f"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Szymkiewicz–Simpson dissimilarity"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmerInvOverlapCoef</span><span class="p">);</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="c"> <span class="p">}</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Chi-square distance */</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4096</span><span class="p">)</span> <span class="p">{</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="c"> <span class="n" style="color: #333;">printIntLtdPhy</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="s" style="color: #d14;">"Chi-square distance"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chi2dist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="c"> <span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="c"> <span class="p">}</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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743
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">runDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">runDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">disk</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">thread_num</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">i</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">;</span></span>
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369
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748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">DB_size</span><span class="p">;</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" 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;">out_size</span><span class="p">,</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">,</span> <span class="n" style="color: #333;">covMat</span><span class="p">;</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfileM</span><span class="p">;</span></span>
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370
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">;</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="c"> <span class="n" style="color: #333;">DistThread</span> <span class="o" style="font-weight: 600;">*</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">threads</span><span class="p">;</span></span>
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371
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="c"> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">DB</span><span class="p">;</span></span>
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372
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754
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="c"> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">;</span></span>
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373
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="c"> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">;</span></span>
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374
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="c"> </span>
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375
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* init */</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outputfilename</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="sc" style="color: #d14;">'-'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="c"> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stdout</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC378" 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="LC379" class="line" lang="c"> <span class="n" style="color: #333;">outfile</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;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="c"> <span class="n" style="color: #333;">outfile</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;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb+"</span><span class="p">);</span></span>
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381
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="c"> <span class="n" style="color: #333;">file_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* load k-mer links from KMA DB */</span></span>
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382
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="s" style="color: #d14;">".comp.b"</span><span class="p">);</span></span>
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383
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">DB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loadValues</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">)))</span> <span class="p">{</span></span>
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384
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764
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<pre style="margin: 0;"> <span id="LC764" 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;">"Wrong format of DB.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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385
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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386
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="c"> <span class="p">}</span></span>
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387
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="c"> <span class="n" style="color: #333;">templatefilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="c"> <span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span><span class="p">;</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="c"> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">N</span><span class="p">)</span> <span class="p">{</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="c"> <span class="p">}</span></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="c"> <span class="n" style="color: #333;">Dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltdMatrix_init</span><span class="p">(</span><span class="n" style="color: #333;">DB_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="c"> </span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get kmer similarities and lengths */</span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="c"> <span class="n" style="color: #333;">kmerSimilarity</span><span class="p">(</span><span class="n" style="color: #333;">DB</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">);</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="c"> <span class="n" style="color: #333;">destroyValues</span><span class="p">(</span><span class="n" style="color: #333;">DB</span><span class="p">);</span></span>
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398
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="c"> </span>
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399
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* load names */</span></span>
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400
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="s" style="color: #d14;">".name"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="772" style="width: 35px; color: rgba(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">@@ -402,36 +772,75 @@ void runDist(char *templatefilename, char *outputfilename, int flag, int format)</td>
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402
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="c"> <span class="n" style="color: #333;">templatefilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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403
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="c"> <span class="n" style="color: #333;">template_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">setQseqs</span><span class="p">(</span><span class="mi" style="color: #099;">1024</span><span class="p">);</span></span>
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="c"> </span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* <span class="idiff left right">k-mer dist, lt</span> */</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">flag</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">kmerDist</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Dist</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">N</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">template_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">format</span></span><span class="p">);</span></span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="c"> <span class="p"><span class="idiff left right">}</span></span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* <span class="idiff left right">allocate output file</span> */</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">DB_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DB</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">DB_size</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="777" 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">
777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">out_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">getPhySize</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">flag</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">format</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DB_size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">ltdMat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">covMat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">name_file</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="778" 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">
778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">outfileM</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mfile</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">out_size</span></span><span class="p"><span class="idiff right">);</span></span></span>
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409
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779
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="c"> </span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* <span class="idiff left right">k-mer shared, lt</span> */</span></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">flag</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">kmerShared</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Dist</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">N</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">template_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">format</span></span><span class="p">);</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* <span class="idiff left right">allocate matrices</span> */</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">N</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">calloc</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">DB_size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff right">)))</span>)</span> <span class="p">{</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">ERROR</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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413
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="c"> <span class="p">}</span></span>
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414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="c"> </span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">/* query cov, asym */</span></span></span>
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416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">flag</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="p"><span class="idiff right">)</span></span> <span class="p">{</span></span>
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417
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">kmerQuery</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfile</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Dist</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">N</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">template_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">format</span></span><span class="p">);</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">disk</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Dist</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ltdMatrix_minit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">DB_size</span></span><span class="p"><span class="idiff right">);</span></span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="c"> <span class="p"><span class="idiff left">}</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">else</span></span> <span class="p">{</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">Dist</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ltdMatrix_init</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">DB_size</span></span><span class="p">);</span></span>
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418
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="c"> <span class="p">}</span></span>
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419
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="c"> </span>
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420
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* template cov, asym */</span></span>
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421
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="p">{</span></span>
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422
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="c"> <span class="n" style="color: #333;">kmerTemplate</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">);</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* thread out */</span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="c"> <span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_num</span><span class="p">;</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* init */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="796" 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">
796
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<pre style="margin: 0;">+<span id="LC796" 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;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">DistThread</span><span class="p">));</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" 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;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="798" 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">
798
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<pre style="margin: 0;">+<span id="LC798" 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;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">format</span><span class="p">;</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" 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;">thread_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_num</span><span class="p">;</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" 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;">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N</span><span class="p">;</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" 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;">ltdMat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltdMat</span><span class="p">;</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" 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;">covMat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">covMat</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="803" 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">
803
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<pre style="margin: 0;">+<span id="LC803" 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;">outfileM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfileM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="804" 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">
804
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<pre style="margin: 0;">+<span id="LC804" 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;">name_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name_file</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="805" 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">
805
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<pre style="margin: 0;">+<span id="LC805" 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;">DB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DB</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="806" 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">
806
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<pre style="margin: 0;">+<span id="LC806" 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;">Dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Dist</span><span class="p">;</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template_name</span><span class="p">;</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">threads</span><span class="p">;</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="c"> <span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="p">;</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* start */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="811" 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">
811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pthread_create</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">threadDist</span><span class="p">,</span> <span class="kr" style="font-weight: 600;">thread</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="812" 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">
812
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<pre style="margin: 0;">+<span id="LC812" 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;">"Error: %d (%s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">errno</span><span class="p">,</span> <span class="n" style="color: #333;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="813" 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">
813
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<pre style="margin: 0;">+<span id="LC813" 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;">"Will continue with %d threads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="814" 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">
814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="815" 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">
815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="c"> <span class="p">}</span></span>
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423
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="c"> <span class="p">}</span></span>
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424
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<td class="diff-line-num new_line old" data-linenumber="817" style="width: 35px; color: rgba(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="LC424" class="line" lang="c"> </span>
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425
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<td class="diff-line-num new_line old" data-linenumber="817" style="width: 35px; color: rgba(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="LC425" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* avg. cov, lt */</span></span>
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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="p">{</span></span>
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427
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="c"> <span class="n" style="color: #333;">kmerAvg</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="817" 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">
817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* start main thread */</span></span>
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<td class="diff-line-num new old_line" data-linenumber="428" 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="818" 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">
818
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<pre style="margin: 0;">+<span id="LC818" 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;">id</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 new old_line" data-linenumber="428" 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="819" 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">
819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="c"> <span class="n" style="color: #333;">threadDist</span><span class="p">(</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="428" 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="820" 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">
820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="c"> </span>
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<td class="diff-line-num new old_line" data-linenumber="428" 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="821" 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">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* join threads */</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="428" 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="822" 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">
822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="kr" style="font-weight: 600;">thread</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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="428" 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="823" 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">
823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* join thread */</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="428" 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="824" 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">
824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pthread_join</span><span class="p">(</span><span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</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="428" 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="825" 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">
825
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<pre style="margin: 0;">+<span id="LC825" 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="428" 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="826" 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">
826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
428
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<td class="diff-line-num new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
827
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC827" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
429
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<td class="diff-line-num new_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
828
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC828" class="line" lang="c"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
430
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<td class="diff-line-num new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
829
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC829" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* clean */</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="431" 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="830" 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">
830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">threads</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="431" 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="831" 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">
831
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<pre style="margin: 0;">+<span id="LC831" 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;">threads</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 new old_line" data-linenumber="431" 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="832" 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">
832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="431" 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="833" 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">
833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="c"> <span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">thread</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="431" 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="834" 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">
834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="431" 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="835" 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">
835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="c"> <span class="n" style="color: #333;">munmap</span><span class="p">(</span><span class="n" style="color: #333;">outfileM</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">out_size</span><span class="p">,</span> <span class="n" style="color: #333;">out_size</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
431
</td>
<td class="diff-line-num new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
836
</td>
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
432
</td>
<td class="diff-line-num new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
837
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC837" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
433
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<td class="diff-line-num new_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
838
</td>
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">N</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
434
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<td class="diff-line-num new_line old" data-linenumber="839" style="width: 35px; color: rgba(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="LC434" class="line" lang="c"> <span class="n" style="color: #333;">Matrix_destroy</span><span class="p">(</span><span class="n" style="color: #333;">Dist</span><span class="p">);</span></span>
</pre>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">disk</span><span class="p">)</span> <span class="p">{</span></span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="c"> <span class="n" style="color: #333;">Matrix_mdestroy</span><span class="p">(</span><span class="n" style="color: #333;">Dist</span><span class="p">);</span></span>
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841
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<pre style="margin: 0;">+<span id="LC841" 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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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="c"> <span class="n" style="color: #333;">Matrix_destroy</span><span class="p">(</span><span class="n" style="color: #333;">Dist</span><span class="p">);</span></span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="c"> <span class="p">}</span></span>
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435
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="c"> <span class="n" style="color: #333;">destroyQseqs</span><span class="p">(</span><span class="n" style="color: #333;">template_name</span><span class="p">);</span></span>
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="c"><span class="p">}</span></span>
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437
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846
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="440" style="width: 35px; color: rgba(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="849" style="width: 35px; color: rgba(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">@@ -440,11 +849,14 @@ static int helpMessage(FILE *out) {</td>
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440
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849
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"#kma dist calculates distances between templates from a kma index</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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441
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Options are:"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Desc:"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Default:"</span><span class="p">);</span></span>
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442
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851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-t_db"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Template DB"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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443
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output file"</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right">stdout</span>"</span><span class="p">);</span></span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output file"</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right">DB</span>"</span><span class="p">);</span></span>
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444
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853
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output flags"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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445
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854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-fh"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Help on option </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-f</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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446
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<td class="diff-line-num new_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-d"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Distance method"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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447
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<td class="diff-line-num new_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-dh"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Help on option </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-d</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Allocate matrix on the disk"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">);</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-tmp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Set directory for temporary files"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-t"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number of threads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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448
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<td class="diff-line-num new_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-h"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Shows this helpmessage"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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449
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861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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450
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862
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="c"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="452" style="width: 35px; color: rgba(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="864" style="width: 35px; color: rgba(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">@@ -452,15 +864,19 @@ static int helpMessage(FILE *out) {</td>
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452
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* main */</span></span>
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453
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">dist_main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>
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454
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="c"> </span>
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455
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="n" style="color: #333;">file_len</span><span class="p">;</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">mmap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">thread_num</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">file_len</span><span class="p">;</span></span>
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456
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorMsg</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">;</span></span>
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457
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="c"> </span>
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458
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* init */</span></span>
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459
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871
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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460
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872
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="c"> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="c"> <span class="n" style="color: #333;">mmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="c"> <span class="n" style="color: #333;">thread_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="c"> <span class="n" style="color: #333;">file_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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461
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876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="c"> <span class="n" style="color: #333;">templatefilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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462
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877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="c"> <span class="n" style="color: #333;">outputfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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463
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878
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="c"> </span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* parse cmd-line */</span></span>
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464
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880
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="c"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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465
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881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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466
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="c"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -491,29 +907,55 @@ int dist_main(int argc, char *argv[]) {</td>
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491
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">"fh"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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492
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Format flags output, add them to combine them.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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493
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"# 1:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Relaxed Phylip</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"# 4:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Include template name in phylip file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"Relaxed Phylip"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="911" 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">
911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="s" style="color: #d14;">"Include distance method(s) in phylip file"</span><span class="p">);</span></span>
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497
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912
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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498
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913
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">"d"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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499
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914
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="c"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtoul</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">errorMsg</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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501
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<td class="diff-line-num new_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
916
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorMsg</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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502
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<td class="diff-line-num new_line old" data-linenumber="917" style="width: 35px; color: rgba(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="LC502" class="line" lang="c"> <span class="n" style="color: #333;">invaArg</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-<span class="idiff left right">f</span></span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="503" 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="917" 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">
917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="c"> <span class="n" style="color: #333;">invaArg</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-<span class="idiff left right">d</span></span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
503
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<td class="diff-line-num new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
918
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
504
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<td class="diff-line-num new_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
919
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<pre style="margin: 0;"> <span id="LC919" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
920
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<pre style="margin: 0;"> <span id="LC920" class="line" lang="c"> <span class="n" style="color: #333;">missArg</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-d</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
921
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<pre style="margin: 0;"> <span id="LC921" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_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">
507
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<td class="diff-line-num new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
922
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<pre style="margin: 0;"> <span id="LC922" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">"dh"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" 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">
508
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<td class="diff-line-num new_line old" data-linenumber="923" style="width: 35px; color: rgba(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="LC508" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Distance calculation methods, add them to combine them:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="923" 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">
923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Distance <span class="idiff left right">/ Similarity </span>calculation methods, add them to combine them:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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509
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<td class="diff-line-num new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
924
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
510
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<td class="diff-line-num new_line old" data-linenumber="925" style="width: 35px; color: rgba(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="LC510" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"# 1:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">k-mer distance</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
511
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<td class="diff-line-num new_line old" data-linenumber="925" style="width: 35px; color: rgba(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="LC511" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"# 2:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Shared k-mers</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
512
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<td class="diff-line-num new_line old" data-linenumber="925" style="width: 35px; color: rgba(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="LC512" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"# 4:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">k-mer query coverage</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
513
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<td class="diff-line-num new_line old" data-linenumber="925" style="width: 35px; color: rgba(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="LC513" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"# 8:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">k-mer template coverage</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
514
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<td class="diff-line-num new_line old" data-linenumber="925" style="width: 35px; color: rgba(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="LC514" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"# 16:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">k-mer avg. coverage</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="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">
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<td class="diff-line-num new new_line" data-linenumber="925" 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">
925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"k-mer hamming distance"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="926" 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">
926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"Shared k-mers"</span><span class="p">);</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="s" style="color: #d14;">"k-mer query coverage"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="928" 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">
928
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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="LC928" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="s" style="color: #d14;">"k-mer template coverage"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="929" 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">
929
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC929" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">,</span> <span class="s" style="color: #d14;">"k-mer avg. coverage"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="930" 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">
930
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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="LC930" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">32</span><span class="p">,</span> <span class="s" style="color: #d14;">"k-mer inv. avg. coverage"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_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">
</td>
<td class="diff-line-num new new_line" data-linenumber="931" 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">
931
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC931" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">,</span> <span class="s" style="color: #d14;">"Jaccard distance"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_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">
</td>
<td class="diff-line-num new new_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
932
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC932" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">128</span><span class="p">,</span> <span class="s" style="color: #d14;">"Jaccard similarity"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_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">
</td>
<td class="diff-line-num new new_line" data-linenumber="933" 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">
933
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC933" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">256</span><span class="p">,</span> <span class="s" style="color: #d14;">"Cosine distance"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_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">
</td>
<td class="diff-line-num new new_line" data-linenumber="934" 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">
934
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC934" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">512</span><span class="p">,</span> <span class="s" style="color: #d14;">"Cosine similarity"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="935" 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">
935
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC935" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">1024</span><span class="p">,</span> <span class="s" style="color: #d14;">"Szymkiewicz–Simpson similarity"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_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">
</td>
<td class="diff-line-num new new_line" data-linenumber="936" 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">
936
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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="LC936" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">2048</span><span class="p">,</span> <span class="s" style="color: #d14;">"Szymkiewicz–Simpson dissimilarity"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_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">
</td>
<td class="diff-line-num new new_line" data-linenumber="937" 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">
937
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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="LC937" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#%9d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">4096</span><span class="p">,</span> <span class="s" style="color: #d14;">"Chi-square distance"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
515
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<td class="diff-line-num new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
938
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC938" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</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="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
516
</td>
<td class="diff-line-num new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
939
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC939" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="517" 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="940" 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">
940
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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="LC940" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">"m"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="517" 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="941" 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">
941
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC941" class="line" lang="c"> <span class="n" style="color: #333;">mmap</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 new old_line" data-linenumber="517" 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="942" 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">
942
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC942" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-tmp"</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="517" 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="943" 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">
943
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC943" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="517" 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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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="c"> <span class="n" style="color: #333;">tmpF</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">]);</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" 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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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="c"> <span class="n" style="color: #333;">invaArg</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-tmp</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="c"> <span class="p">}</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="c"> <span class="p">}</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-t"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="952" 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">
952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="c"> <span class="n" style="color: #333;">thread_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtoul</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">errorMsg</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorMsg</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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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="c"> <span class="n" style="color: #333;">invaArg</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-t</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="956" 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">
956
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<pre style="margin: 0;">+<span id="LC956" 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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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="c"> <span class="n" style="color: #333;">missArg</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-t</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="c"> <span class="p">}</span></span>
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517
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959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">"h"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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518
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">helpMessage</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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519
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<td class="diff-line-num new_line" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="532" style="width: 35px; color: rgba(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="974" style="width: 35px; color: rgba(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">@@ -532,10 +974,11 @@ int dist_main(int argc, char *argv[]) {</td>
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532
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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533
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975
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="c"> <span class="p">}</span></span>
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534
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">outputfilename</span><span class="p">)</span> <span class="p">{</span></span>
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535
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="c"> <span class="n" style="color: #333;">outputfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"--"</span><span class="p">;</span></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="c"> <span class="n" style="color: #333;">outputfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">file_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.phy"</span><span class="p">,</span> <span class="n" style="color: #333;">templatefilename</span><span class="p">);</span></span>
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536
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979
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<pre style="margin: 0;"> <span id="LC979" class="line" lang="c"> <span class="p">}</span></span>
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537
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980
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<pre style="margin: 0;"> <span id="LC980" class="line" lang="c"> </span>
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538
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="c"> <span class="n" style="color: #333;">runDist</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p">);</span></span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="c"> <span class="n" style="color: #333;">runDist</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mmap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">thread_num</span></span><span class="p">);</span></span>
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539
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982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="c"> </span>
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540
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983
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<pre style="margin: 0;"> <span id="LC983" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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541
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984
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<pre style="margin: 0;"> <span id="LC984" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/694b4807c99bddd1372450e2a4ecc175f482e50f#a9c0f53d72073d487e5f909ae155567290a2a5fa"><strong>dist.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,6 +19,7 @@</td>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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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 _XOPEN_SOURCE 600</span></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <limits.h></span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <pthread.h></span></span>
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22
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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23
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,13 +28,47 @@</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "pherror.h"</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "runkma.h"</span></span>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef DIST</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">distThread</span> <span class="n" style="color: #333;">DistThread</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">distThread</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">pthread_t</span> <span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" 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;">ltdMat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" 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;">covMat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfileM</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">DB</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">distThread</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define DIST 1</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"><span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">loadValues</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">destroyValues</span><span class="p">(</span><span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerSimilarity</span><span class="p">(</span><span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">DB</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerShared</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerQuery</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerTemplate</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerAvg</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">runDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">kmerSimilarity_thread</span><span class="p">(</span><span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">DB</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">kmerDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">kmerShared</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">chi2dist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printIntLtdPhy</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">method</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">distPtr</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerQuery</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerTemplate</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerAvg</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="62" 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">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerInvAvg</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerJaccardDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="64" 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">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerJaccardSim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerCosineDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerCosineSim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerOverlapCoef</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">kmerInvOverlapCoef</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Ni</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Nj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">D</span><span class="p">);</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printDoublePhy</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">N</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">formatString</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ltd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">method</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">distPtr</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" 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="nf" style="color: #900; font-weight: 600;">getPhySize</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</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;">n</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ltdMat</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">covMat</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">mfile</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outfile</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;">size</span><span class="p">);</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">threadDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arg</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">runDist</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">disk</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">dist_main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">[]);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/694b4807c99bddd1372450e2a4ecc175f482e50f#4a59da3f123fbc2eabd4b7c4d9c4e2f54d6af662"><strong>kmers.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -104,18 +104,28 @@ int save_kmers_batch(char *templatefilename, char *exePrev, unsigned shm, int th</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">deConPrintPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">printPtr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">prefix_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">get_kmers_for_pair_ptr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">get_kmers_for_pair_count</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* here */</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if(kmerScan == &save_kmers) {</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> kmerScan = &save_kmers_pseuodeSparse;</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> kmerScan = &save_kmers_sparse_chain;</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">kmerScan</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">save_kmers_pseuodeSparse</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">get_kmers_for_pair_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">get_kmers_for_pair_pseoudoSparse</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC118" 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="LC119" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* here */</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if(kmerScan == &save_kmers) {</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> kmerScan = &save_kmers_Sparse;</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> kmerScan = &save_kmers_sparse_chain;</span></span>
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">kmerScan</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">save_kmers_Sparse</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">get_kmers_for_pair_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">get_kmers_for_pair_Sparse</span><span class="p">;</span></span>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/694b4807c99bddd1372450e2a4ecc175f482e50f#43638494320234f912fa37977d784743664b2c37"><strong>matrix.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,9 +17,15 @@</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _XOPEN_SOURCE 600</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <limits.h></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/mman.h></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/param.h></span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "matrix.h"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "pherror.h"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "tmp.h"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">matrix_init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,7 +60,7 @@ Matrix * ltdMatrix_init(unsigned size) {</td>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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56
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</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;"><span class="idiff left right">size</span></span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">*</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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58
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!*</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">))</span> <span class="p">{</span></span>
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59
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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60
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,11 +78,50 @@ Matrix * ltdMatrix_init(unsigned size) {</td>
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72
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dest</span><span class="p">;</span></span>
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73
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"><span class="p">}</span></span>
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74
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ltdMatrix_minit</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;">size</span><span class="p">)</span> <span class="p">{</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"> </span>
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83
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<pre style="margin: 0;">+<span id="LC83" 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;">n</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">;</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">;</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span><span class="p">));</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">size</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;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> </span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get matrix */</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpF</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</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="n" style="color: #333;">putc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EOF</span><span class="p">)</span> <span class="p">{</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"> <span class="p">}</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">tmp</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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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mmap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">PROT_READ</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">PROT_WRITE</span><span class="p">,</span> <span class="n" style="color: #333;">MAP_SHARED</span><span class="p">,</span> <span class="n" style="color: #333;">fileno</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">),</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">MAP_FAILED</span><span class="p">)</span> <span class="p">{</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">posix_madvise</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">),</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">POSIX_MADV_SEQUENTIAL</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* set matrix rows */</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">ptr</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;">mat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">src</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ptr</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">src</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="p">}</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> </span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dest</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"><span class="p">}</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ltdMatrix_realloc</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC122" 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="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mat</span><span class="p">;</span></span>
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"> <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;">mat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">realloc</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;">mat</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;"><span class="idiff left right">size</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_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="LC124" class="line" lang="c"> <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;">mat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">realloc</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;">mat</span><span class="p">),</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">*</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">realloc</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;">mat</span><span class="p">,</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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81
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!*</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -96,6 +141,14 @@ void ltdMatrix_realloc(Matrix *src, unsigned size) {</td>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">Matrix_destroy</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">free</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;">mat</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">free</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;">mat</span><span class="p">);</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"><span class="p">}</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">Matrix_mdestroy</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</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>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> <span class="n" style="color: #333;">munmap</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;">mat</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;">size</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">free</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;">mat</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"><span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,9 @@ struct matrix {</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">matrix_init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ltdMatrix_init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ltdMatrix_minit</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;">size</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ltdMatrix_realloc</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">Matrix_destroy</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">Matrix_mdestroy</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ltdMatrix_popArrange</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mat</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ltdMatrix_add</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/694b4807c99bddd1372450e2a4ecc175f482e50f#ca9efd475143efe0a1b0464c67f49900d98ca75a"><strong>runkma.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1250,6 +1250,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1251" 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="LC1252" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ID_t</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">templates_index</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC1254" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_file</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="c"> <span class="n" style="color: #333;">assembly_KMA_Ptr</span><span class="p">(</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/694b4807c99bddd1372450e2a4ecc175f482e50f#f9ead8e7fb7b1680f786604627e0ac2147f4b7ef"><strong>savekmers.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +37,7 @@</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "threader.h"</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ankerPtr</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ankerAndClean</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kmerScan</span><span class="p">)(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">save_kmers_<span class="idiff left">chain</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//&save_kmers_HMM</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kmerScan</span><span class="p">)(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">save_kmers_<span class="idiff left">HMM</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff">/* here */</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//&save_kmers_chain</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">save_kmers_pair</span><span class="p">)(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">save_kmers_unionPair</span><span class="p">;</span></span>
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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">get_kmers_for_pair_ptr</span><span class="p">)(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">get_kmers_for_pair</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">getMatch</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">getBestMatch</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/694b4807c99bddd1372450e2a4ecc175f482e50f#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4"><strong>version.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,4 +17,4 @@</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.<span class="idiff left right">0</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.<span class="idiff left right">2</span>"</span></span></pre>
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