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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/gmap">Debian Med / gmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/d3ac61590603dc6f86f34dfb6b49583676d0c14c">d3ac6159</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-19T16:31:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/0ba0084d34b8453a7c19ded1b3b6bf3e3743d358">0ba0084d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-19T16:31:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021-02-12+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/1964c1d14d903598b4e5a6e0ec926f6bec6fc38b">1964c1d1</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-19T16:32:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2021-02-12+ds'
Update to upstream version '2021-02-12+ds'
with Debian dir e9b5654cdbbcecca4850ca448a41b7f237d081c1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af">a691ebb5</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-19T16:34:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
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</li>
<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#39f73f3fcab5e56bf327190a099c346bb4c38598">
src/filestring.c
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<li class="file-stats">
<a href="#49786cab443f0fbab3b5bb48f2f310040d725d74">
src/genome128_hr.c
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</li>
<li class="file-stats">
<a href="#d747f527041a6e797f86fcd6f1fcd1562bab24a2">
src/gmap.c
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</li>
<li class="file-stats">
<a href="#d1a71d80a50c38c9cb493f24be3edf3b17c8f562">
src/gsnap.c
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<li class="file-stats">
<a href="#533dac6a70f6f1a9e019d374052128e93650f659">
src/outbuffer.c
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<li class="file-stats">
<a href="#c672fce9c671440792e33117e131e53e07e9ddc6">
src/output.c
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<li class="file-stats">
<a href="#41c3f2188ff05d862f9f803bd84d0d1d705983fa">
src/resulthr.c
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<li class="file-stats">
<a href="#2d331dd15dccff926559b191048c3a7d2d3a5fae">
src/stage3hr.c
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<li class="file-stats">
<a href="#1f55d42fa4aff8ae5015454067ccb1a098a3964e">
src/stage3hr.h
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</li>
</ul>
<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="">2021-02-14 twu</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang=""> * index.html: Updated for latest version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang=""> * outbuffer.c: Added comment</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="">2021-02-13 twu</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang=""> * outbuffer.c: Calling setvbuf before printing file headers</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang=""> * gmap.c, gsnap.c: Added comments</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang=""> * output.c: Fixed code for deciding on failed input for single-end reads</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang=""> * VERSION, index.html: Updated version number</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang=""> * output.c: Using the results of Stage3pair_print_end to determine whether a</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang=""> sequence failed to print</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang=""> * stage3hr.c, stage3hr.h: Stage3pair_print_end now returns whether it</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang=""> printed an alignment</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang=""> * gsnap.c: Formatting change</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang=""> * genome128_hr.c: Removed extraneous semicolon at end of macro</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang=""> * outbuffer.c: Checking for a NULL string from Filestring_T before pushing</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang=""> onto the failedinput Filestring_T</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang=""> * resulthr.c: Fixed a memory leak</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang=""> * filestring.c: Removed faulty assertion</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="">2020-12-16 twu</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang=""> * outbuffer.c: Added option for using write instead of fwrite</span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2020-12-17</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2021-02-12</span></pre>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">gmap (202<span class="idiff left right">0-12-17+ds-3) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gmap (202<span class="idiff left right">1-02-12+ds-1) unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Apply patch from Helmut Grohne for slightly better cross building</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> support. Closes: #980484</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * New upstream release.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> <span class="idiff left right">Tue, 19 Jan 2021 20:09:11</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> <span class="idiff left right">Fri, 19 Feb 2021 16:32:15</span> +0100</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">gmap (2020-12-17+ds-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#39f73f3fcab5e56bf327190a099c346bb4c38598"><strong>src/filestring.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: filestring.c 223<span class="idiff left right">773 2020-12-14 19:15:02</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: filestring.c 223<span class="idiff left right">803 2021-02-13 17:17:15</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -63,7 +63,9 @@ Filestring_split_output (T this) {</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Filestring_string</span> <span class="p">(</span><span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">this</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* Because we assume that Filestring_stringify has been called */</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Because we assume that Filestring_stringify has been called */</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* But could be NULL */</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* assert(this->string != NULL); */</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#49786cab443f0fbab3b5bb48f2f310040d725d74"><strong>src/genome128_hr.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: genome128_hr.c 223<span class="idiff left right">551 2020-11-15 19:43:52</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: genome128_hr.c 223<span class="idiff left right">806 2021-02-13 18:45:39</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -4186,7 +4186,7 @@ clear_lowbit_128 (__m128i _diff, int relpos) {</td>
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4186
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<pre style="margin: 0;"> <span id="LC4186" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define clear_highbit_32(diff,relpos) (diff ^ (HIGH_BIT >> relpos))</span></span>
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4187
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4187
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<pre style="margin: 0;"> <span id="LC4187" class="line" lang="c"></span>
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4188
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<pre style="margin: 0;"> <span id="LC4188" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Slower: clear_lowbit(diff,relpos) diff -= (1 << relpos) */</span></span>
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4189
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<pre style="margin: 0;">-<span id="LC4189" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define clear_lowbit_32(diff,relpos) (diff & (diff - 1))<span class="idiff left right">;</span></span></span>
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<pre style="margin: 0;">+<span id="LC4189" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define clear_lowbit_32(diff,relpos) (diff & (diff - 1))</span></span>
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4190
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<pre style="margin: 0;"> <span id="LC4190" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC4191" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC4192" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if !defined(HAVE_SSE4_2)</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#d747f527041a6e797f86fcd6f1fcd1562bab24a2"><strong>src/gmap.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: gmap.c 223<span class="idiff left right">772 2020-12-14 19:14:33</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: gmap.c 223<span class="idiff left right">812 2021-02-14 00:01:36</span>Z twu $"</span><span class="p">;</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -4863,6 +4863,7 @@ worker_thread (void *data) {</td>
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<pre style="margin: 0;"> <span id="LC4863" class="line" lang="c"> <span class="n" style="color: #333;">Stopwatch_T</span> <span class="n" style="color: #333;">worker_stopwatch</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4864" class="line" lang="c"> <span class="n" style="color: #333;">Request_T</span> <span class="n" style="color: #333;">request</span><span class="p">;</span></span>
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4865
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4865
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<pre style="margin: 0;"> <span id="LC4865" class="line" lang="c"> <span class="n" style="color: #333;">Genome_T</span> <span class="n" style="color: #333;">genome</span><span class="p">,</span> <span class="n" style="color: #333;">genomealt</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4866" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Outbuffer_lines_T lines; -- For multithreaded, Output_thread_ordered and Output_thread_anyorder create lines */</span></span>
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4866
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4867
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<pre style="margin: 0;"> <span id="LC4867" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_T</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">fp_failedinput</span><span class="p">;</span></span>
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4867
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4868
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<pre style="margin: 0;"> <span id="LC4868" class="line" lang="c"> <span class="n" style="color: #333;">Sequence_T</span> <span class="n" style="color: #333;">queryseq</span><span class="p">;</span></span>
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4868
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4869
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<pre style="margin: 0;"> <span id="LC4869" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">worker_jobid</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 unfold js-unfold new_line" data-linenumber="4952" style="width: 35px; color: rgba(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">@@ -4951,6 +4952,8 @@ worker_thread (void *data) {</td>
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4951
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4952
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<pre style="margin: 0;"> <span id="LC4952" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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4952
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4953
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<pre style="margin: 0;"> <span id="LC4953" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_stringify</span><span class="p">(</span><span class="n" style="color: #333;">fp_failedinput</span><span class="p">);</span></span>
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4953
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4954
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<pre style="margin: 0;"> <span id="LC4954" class="line" lang="c"> <span class="p">}</span></span>
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4955
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<pre style="margin: 0;">+<span id="LC4955" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC4956" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* For multithreaded, let Outbuffer_thread_ordered and Outbuffer_thread_anyordered call Outbuffer_lines_store */</span></span>
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4954
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4957
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<pre style="margin: 0;"> <span id="LC4957" class="line" lang="c"> <span class="n" style="color: #333;">Outbuffer_put_filestrings</span><span class="p">(</span><span class="n" style="color: #333;">outbuffer</span><span class="p">,</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">fp_failedinput</span><span class="p">);</span></span>
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4958
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<pre style="margin: 0;"> <span id="LC4958" class="line" lang="c"></span>
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4959
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<pre style="margin: 0;"> <span id="LC4959" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">worker_jobid</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">POOL_FREE_INTERVAL</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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<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#d1a71d80a50c38c9cb493f24be3edf3b17c8f562"><strong>src/gsnap.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: gsnap.c 223<span class="idiff left right">772 2020-12-14 19:14:33</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: gsnap.c 223<span class="idiff left right">812 2021-02-14 00:01:36</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -1209,8 +1209,7 @@ single_thread () {</td>
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1209
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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="c"> <span class="p">}</span></span>
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1210
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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="c"></span>
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1211
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Previously called Outbuffer_print_filestrings */</span></span>
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1212
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<pre style="margin: 0;">-<span id="LC1212" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Outbuffer_lines_store</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fp_failedinput</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fp_failedinput_1</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span></span>
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1213
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<pre style="margin: 0;">-<span id="LC1213" class="line" lang="c"> <span class="n" style="color: #333;">output_buffer_size</span><span class="p">)</span> <span class="p">{</span></span>
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1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Outbuffer_lines_store</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fp_failedinput</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fp_failedinput_1</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">output_buffer_size</span><span class="p">)</span> <span class="p">{</span></span>
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1214
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1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="c"> <span class="n" style="color: #333;">Outbuffer_lines_print</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">);</span></span>
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1215
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1214
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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="c"> <span class="p">}</span></span>
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1216
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1215
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<pre style="margin: 0;"> <span id="LC1215" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1300" style="width: 35px; color: rgba(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="1299" style="width: 35px; color: rgba(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">@@ -1300,6 +1299,7 @@ single_thread () {</td>
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1300
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1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span></span>
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1301
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1300
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">worker_thread</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;">data</span><span class="p">)</span> <span class="p">{</span></span>
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1302
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1301
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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="c"> <span class="n" style="color: #333;">Request_T</span> <span class="n" style="color: #333;">request</span><span class="p">;</span></span>
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1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Outbuffer_lines_T lines; -- For multithreaded, Output_thread_ordered and Output_thread_anyorder create lines */</span></span>
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1303
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1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_T</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">fp_failedinput</span><span class="p">,</span> <span class="n" style="color: #333;">fp_failedinput_1</span><span class="p">,</span> <span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">;</span></span>
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1304
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1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="c"> <span class="n" style="color: #333;">Shortread_T</span> <span class="n" style="color: #333;">queryseq1</span><span class="p">;</span></span>
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1305
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1305
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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="c"> <span class="n" style="color: #333;">Stopwatch_T</span> <span class="n" style="color: #333;">worker_stopwatch</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1423" style="width: 35px; color: rgba(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="1423" style="width: 35px; color: rgba(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">@@ -1423,6 +1423,8 @@ worker_thread (void *data) {</td>
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1423
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1423
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<pre style="margin: 0;"> <span id="LC1423" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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1424
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1424
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<pre style="margin: 0;"> <span id="LC1424" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_stringify</span><span class="p">(</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">);</span></span>
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1425
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1425
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<pre style="margin: 0;"> <span id="LC1425" class="line" lang="c"> <span class="p">}</span></span>
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1426
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<pre style="margin: 0;">+<span id="LC1426" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1427
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<pre style="margin: 0;">+<span id="LC1427" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* For multithreaded, let Outbuffer_thread_ordered and Outbuffer_thread_anyordered call Outbuffer_lines_store */</span></span>
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1426
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1428
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<pre style="margin: 0;"> <span id="LC1428" class="line" lang="c"> <span class="n" style="color: #333;">Outbuffer_put_filestrings</span><span class="p">(</span><span class="n" style="color: #333;">outbuffer</span><span class="p">,</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">fp_failedinput</span><span class="p">,</span><span class="n" style="color: #333;">fp_failedinput_1</span><span class="p">,</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">);</span></span>
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1427
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1429
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<pre style="margin: 0;"> <span id="LC1429" class="line" lang="c"></span>
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1428
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1430
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<pre style="margin: 0;"> <span id="LC1430" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">worker_jobid</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">POOL_FREE_INTERVAL</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3658" style="width: 35px; color: rgba(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="3660" style="width: 35px; color: rgba(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">@@ -3658,12 +3660,6 @@ main (int argc, char *argv[]) {</td>
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3658
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3660
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<pre style="margin: 0;"> <span id="LC3660" class="line" lang="c"> <span class="n" style="color: #333;">FREE</span><span class="p">(</span><span class="n" style="color: #333;">dbversion</span><span class="p">);</span></span>
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3659
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<td class="diff-line-num new_line" data-linenumber="3661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3661
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<pre style="margin: 0;"> <span id="LC3661" class="line" lang="c"> <span class="n" style="color: #333;">chromosome_iit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chromosome_iit_setup</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genomelength</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nchromosomes</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">circular_typeint</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">any_circular_p</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">circularp</span><span class="p">,</span></span>
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3660
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3662
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<pre style="margin: 0;"> <span id="LC3662" class="line" lang="c"> <span class="n" style="color: #333;">genomesubdir</span><span class="p">,</span><span class="n" style="color: #333;">genome_fileroot</span><span class="p">);</span></span>
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3661
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<pre style="margin: 0;">-<span id="LC3661" class="line" lang="c"> <span class="n" style="color: #333;">Outbuffer_setup</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">,</span><span class="n" style="color: #333;">optind</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span><span class="n" style="color: #333;">any_circular_p</span><span class="p">,</span></span>
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3662
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<pre style="margin: 0;">-<span id="LC3662" class="line" lang="c"> <span class="n" style="color: #333;">nthreads</span><span class="p">,</span><span class="n" style="color: #333;">orderedp</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span></span>
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3663
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<pre style="margin: 0;">-<span id="LC3663" class="line" lang="c"> <span class="n" style="color: #333;">output_type</span><span class="p">,</span><span class="n" style="color: #333;">sam_headers_p</span><span class="p">,</span><span class="n" style="color: #333;">sam_read_group_id</span><span class="p">,</span><span class="n" style="color: #333;">sam_read_group_name</span><span class="p">,</span></span>
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3664
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<pre style="margin: 0;">-<span id="LC3664" class="line" lang="c"> <span class="n" style="color: #333;">sam_read_group_library</span><span class="p">,</span><span class="n" style="color: #333;">sam_read_group_platform</span><span class="p">,</span></span>
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3665
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<pre style="margin: 0;">-<span id="LC3665" class="line" lang="c"> <span class="n" style="color: #333;">paired_end_p</span><span class="p">,</span><span class="n" style="color: #333;">appendp</span><span class="p">,</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span><span class="n" style="color: #333;">split_output_root</span><span class="p">,</span><span class="n" style="color: #333;">failedinput_root</span><span class="p">);</span></span>
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3666
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<pre style="margin: 0;">-<span id="LC3666" class="line" lang="c"></span>
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3667
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3663
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<pre style="margin: 0;"> <span id="LC3663" class="line" lang="c"></span>
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3668
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3664
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<pre style="margin: 0;"> <span id="LC3664" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transcriptome_dbroot</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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3669
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3665
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<pre style="margin: 0;"> <span id="LC3665" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">user_transcriptomedir</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">user_genomedir</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</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="3692" style="width: 35px; color: rgba(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="3688" style="width: 35px; color: rgba(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">@@ -3692,6 +3688,13 @@ main (int argc, char *argv[]) {</td>
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3692
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3688
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<pre style="margin: 0;"> <span id="LC3688" 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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3693
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<pre style="margin: 0;"> <span id="LC3689" class="line" lang="c"> <span class="p">}</span></span>
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3694
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3690
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<pre style="margin: 0;"> <span id="LC3690" class="line" lang="c"></span>
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3691
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<pre style="margin: 0;">+<span id="LC3691" class="line" lang="c"></span>
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3692
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<pre style="margin: 0;">+<span id="LC3692" class="line" lang="c"> <span class="n" style="color: #333;">Outbuffer_setup</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">,</span><span class="n" style="color: #333;">optind</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span><span class="n" style="color: #333;">any_circular_p</span><span class="p">,</span></span>
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3693
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<pre style="margin: 0;">+<span id="LC3693" class="line" lang="c"> <span class="n" style="color: #333;">nthreads</span><span class="p">,</span><span class="n" style="color: #333;">orderedp</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC3694" class="line" lang="c"> <span class="n" style="color: #333;">output_type</span><span class="p">,</span><span class="n" style="color: #333;">sam_headers_p</span><span class="p">,</span><span class="n" style="color: #333;">sam_read_group_id</span><span class="p">,</span><span class="n" style="color: #333;">sam_read_group_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC3695" class="line" lang="c"> <span class="n" style="color: #333;">sam_read_group_library</span><span class="p">,</span><span class="n" style="color: #333;">sam_read_group_platform</span><span class="p">,</span></span>
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3696
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<pre style="margin: 0;">+<span id="LC3696" class="line" lang="c"> <span class="n" style="color: #333;">paired_end_p</span><span class="p">,</span><span class="n" style="color: #333;">appendp</span><span class="p">,</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span><span class="n" style="color: #333;">split_output_root</span><span class="p">,</span><span class="n" style="color: #333;">failedinput_root</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC3697" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC3698" class="line" lang="c"> <span class="n" style="color: #333;">outbuffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Outbuffer_new</span><span class="p">(</span><span class="n" style="color: #333;">output_buffer_size</span><span class="p">,</span><span class="n" style="color: #333;">nread</span><span class="p">);</span></span>
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3696
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3699
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<pre style="margin: 0;"> <span id="LC3699" class="line" lang="c"> <span class="n" style="color: #333;">Inbuffer_set_outbuffer</span><span class="p">(</span><span class="n" style="color: #333;">inbuffer</span><span class="p">,</span><span class="n" style="color: #333;">outbuffer</span><span class="p">);</span></span>
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3697
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3700
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<pre style="margin: 0;"> <span id="LC3700" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#533dac6a70f6f1a9e019d374052128e93650f659"><strong>src/outbuffer.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: outbuffer.c 223<span class="idiff left right">787 2020-12-16 16:18:27</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: outbuffer.c 223<span class="idiff left right">814 2021-02-14 17:59:44</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,7 +39,11 @@ static char rcsid[] = "$Id: outbuffer.c 223787 2020-12-16 16:18:27Z twu $";</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> fewer system calls. */</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define OUTPUTLEN 65536</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define USE_WRITE 0 </span><span class="cm" style="color: #998; font-style: italic;">/* Use write instead of fwrite. May not be portable. */</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Use write instead of fwrite. May not be portable, and is als not</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> thread-safe, so it can cause a race condition where alignment</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> output is printed before headers. Therefore, do not use */</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* #define USE_WRITE 0 */</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* sam-to-bam conversions always need the headers */</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;">#define SAM_HEADERS_ON_EMPTY_FILES 1</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="524" style="width: 35px; color: rgba(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">@@ -520,10 +524,10 @@ touch_all_single_outputs (FILE **outputs, char *split_output_root, bool appendp)</td>
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520
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524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
521
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<td class="diff-line-num new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="c"> <span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAM_header_fopen</span><span class="p">(</span><span class="n" style="color: #333;">split_output</span><span class="p">,</span><span class="n" style="color: #333;">split_output_root</span><span class="p">,</span><span class="n" style="color: #333;">paired_end_p</span><span class="p">,</span><span class="n" style="color: #333;">appendp</span><span class="p">);</span></span>
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522
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="c"> <span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</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="n" style="color: #333;">MALLOC_KEEP</span><span class="p">(</span><span class="n" style="color: #333;">OUTPUTLEN</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;">char</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="n" style="color: #333;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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524
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SAM_HEADERS_ON_EMPTY_FILES</span></span>
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525
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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;">print_file_headers</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]);</span></span>
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526
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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527
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="c"> <span class="p">}</span></span>
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528
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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;">split_output</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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529
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533
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<pre style="margin: 0;"> <span id="LC533" 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="535" style="width: 35px; color: rgba(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="539" style="width: 35px; color: rgba(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">@@ -535,10 +539,10 @@ touch_all_single_outputs (FILE **outputs, char *split_output_root, bool appendp)</td>
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535
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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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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536
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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;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAM_header_fopen</span><span class="p">(</span><span class="n" style="color: #333;">split_output</span><span class="p">,</span><span class="n" style="color: #333;">split_output_root</span><span class="p">,</span><span class="n" style="color: #333;">paired_end_p</span><span class="p">,</span><span class="n" style="color: #333;">appendp</span><span class="p">);</span></span>
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537
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="c"> <span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</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="n" style="color: #333;">MALLOC_KEEP</span><span class="p">(</span><span class="n" style="color: #333;">OUTPUTLEN</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;">char</span><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="n" style="color: #333;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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539
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SAM_HEADERS_ON_EMPTY_FILES</span></span>
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540
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="c"> <span class="n" style="color: #333;">print_file_headers</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]);</span></span>
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541
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544
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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542
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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>
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543
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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;">split_output</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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544
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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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="549" style="width: 35px; color: rgba(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="553" style="width: 35px; color: rgba(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">@@ -549,10 +553,10 @@ touch_all_single_outputs (FILE **outputs, char *split_output_root, bool appendp)</td>
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549
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553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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550
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<td class="diff-line-num new_line" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="c"> <span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAM_header_fopen</span><span class="p">(</span><span class="n" style="color: #333;">split_output</span><span class="p">,</span><span class="n" style="color: #333;">split_output_root</span><span class="p">,</span><span class="n" style="color: #333;">paired_end_p</span><span class="p">,</span><span class="n" style="color: #333;">appendp</span><span class="p">);</span></span>
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551
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555
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="c"> <span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</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="n" style="color: #333;">MALLOC_KEEP</span><span class="p">(</span><span class="n" style="color: #333;">OUTPUTLEN</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;">char</span><span class="p">));</span></span>
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552
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="c"> <span class="n" style="color: #333;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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553
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SAM_HEADERS_ON_EMPTY_FILES</span></span>
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554
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c"> <span class="n" style="color: #333;">print_file_headers</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]);</span></span>
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555
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="c"> <span class="n" style="color: #333;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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556
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="c"> <span class="p">}</span></span>
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557
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="c"> <span class="n" style="color: #333;">split_output</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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558
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562
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<pre style="margin: 0;"> <span id="LC562" 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="571" style="width: 35px; color: rgba(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="575" style="width: 35px; color: rgba(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">@@ -571,10 +575,10 @@ touch_all_paired_outputs (FILE **outputs, char *split_output_root, bool appendp)</td>
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571
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">split_output</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">N_SPLIT_OUTPUTS_STD</span><span class="p">)</span> <span class="p">{</span></span>
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572
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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;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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573
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="c"> <span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAM_header_fopen</span><span class="p">(</span><span class="n" style="color: #333;">split_output</span><span class="p">,</span><span class="n" style="color: #333;">split_output_root</span><span class="p">,</span><span class="n" style="color: #333;">paired_end_p</span><span class="p">,</span><span class="n" style="color: #333;">appendp</span><span class="p">);</span></span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="c"> <span class="n" style="color: #333;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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575
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SAM_HEADERS_ON_EMPTY_FILES</span></span>
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576
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="c"> <span class="n" style="color: #333;">print_file_headers</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]);</span></span>
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577
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="c"> <span class="n" style="color: #333;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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578
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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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579
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="c"> <span class="n" style="color: #333;">split_output</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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580
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584
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<pre style="margin: 0;"> <span id="LC584" 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="585" style="width: 35px; color: rgba(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="589" style="width: 35px; color: rgba(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">@@ -585,10 +589,10 @@ touch_all_paired_outputs (FILE **outputs, char *split_output_root, bool appendp)</td>
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585
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">split_output</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">N_SPLIT_OUTPUTS_TOCIRC</span><span class="p">)</span> <span class="p">{</span></span>
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586
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590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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587
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="c"> <span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAM_header_fopen</span><span class="p">(</span><span class="n" style="color: #333;">split_output</span><span class="p">,</span><span class="n" style="color: #333;">split_output_root</span><span class="p">,</span><span class="n" style="color: #333;">paired_end_p</span><span class="p">,</span><span class="n" style="color: #333;">appendp</span><span class="p">);</span></span>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="c"> <span class="n" style="color: #333;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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589
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592
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SAM_HEADERS_ON_EMPTY_FILES</span></span>
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590
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="c"> <span class="n" style="color: #333;">print_file_headers</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]);</span></span>
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591
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="c"> <span class="n" style="color: #333;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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592
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596
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="c"> <span class="p">}</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;">split_output</span><span class="o" style="font-weight: 600;">++</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="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">@@ -598,10 +602,10 @@ touch_all_paired_outputs (FILE **outputs, char *split_output_root, bool appendp)</td>
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598
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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;">while</span> <span class="p">(</span><span class="n" style="color: #333;">split_output</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">N_SPLIT_OUTPUTS</span><span class="p">)</span> <span class="p">{</span></span>
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599
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<td class="diff-line-num new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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600
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<td class="diff-line-num new_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="c"> <span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAM_header_fopen</span><span class="p">(</span><span class="n" style="color: #333;">split_output</span><span class="p">,</span><span class="n" style="color: #333;">split_output_root</span><span class="p">,</span><span class="n" style="color: #333;">paired_end_p</span><span class="p">,</span><span class="n" style="color: #333;">appendp</span><span class="p">);</span></span>
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601
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<td class="diff-line-num new_line old" data-linenumber="605" 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="LC601" class="line" lang="c"> <span class="n" style="color: #333;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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602
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SAM_HEADERS_ON_EMPTY_FILES</span></span>
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603
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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;">print_file_headers</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">]);</span></span>
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604
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="c"> <span class="n" style="color: #333;">setvbuf</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">buffer_outputs</span><span class="p">[</span><span class="n" style="color: #333;">split_output</span><span class="p">],</span><span class="n" style="color: #333;">_IOFBF</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUTLEN</span><span class="p">);</span></span>
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605
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="c"> <span class="p">}</span></span>
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606
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="c"> <span class="n" style="color: #333;">split_output</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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607
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611
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<pre style="margin: 0;"> <span id="LC611" 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="815" style="width: 35px; color: rgba(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="819" style="width: 35px; color: rgba(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">@@ -815,8 +819,8 @@ Outbuffer_print_filestrings (Filestring_T fp, Filestring_T fp_failedinput, Files</td>
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815
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> print_file_headers(stdout);</span></span>
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816
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> } else {</span></span>
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817
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<td class="diff-line-num new_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
821
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> output = outputs[0] = SAM_header_fopen(/*split_output*/OUTPUT_FILE,output_file,paired_end_p,appendp);</span></span>
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818
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<td class="diff-line-num new_line old" data-linenumber="822" 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="LC818" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);</span></span>
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819
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822
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> print_file_headers(output);</span></span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);</span></span>
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820
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824
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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821
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825
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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822
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826
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="841" style="width: 35px; color: rgba(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="845" style="width: 35px; color: rgba(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">@@ -841,7 +845,7 @@ Outbuffer_print_filestrings (Filestring_T fp, Filestring_T fp_failedinput, Files</td>
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841
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> return;</span></span>
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842
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846
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">}</span></span>
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843
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847
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="c"></span>
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844
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#el<span class="idiff left right">se</span></span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#el<span class="idiff left right">if 0</span></span></span>
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845
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849
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">void</span></span>
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846
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">Outbuffer_print_filestrings (Filestring_T fp, Filestring_T fp_failedinput) {</span></span>
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847
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851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> SAM_split_output_type split_output;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="863" style="width: 35px; color: rgba(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="867" style="width: 35px; color: rgba(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">@@ -863,12 +867,12 @@ Outbuffer_print_filestrings (Filestring_T fp, Filestring_T fp_failedinput) {</td>
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863
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867
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<pre style="margin: 0;"> <span id="LC867" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> } else if ((output = outputs[0]) == NULL) {</span></span>
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864
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if (output_file == NULL) {</span></span>
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865
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> output = outputs[0] = stdout;</span></span>
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866
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<pre style="margin: 0;">-<span id="LC866" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);</span></span>
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867
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> print_file_headers(stdout);</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);</span></span>
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868
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872
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> } else {</span></span>
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869
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> output = outputs[0] = SAM_header_fopen(/*split_output*/OUTPUT_FILE,output_file,paired_end_p,appendp);</span></span>
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870
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);</span></span>
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871
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> print_file_headers(output);</span></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);</span></span>
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876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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873
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877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="936" style="width: 35px; color: rgba(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">@@ -936,6 +940,7 @@ Outbuffer_lines_store (Outbuffer_lines_T this, Filestring_T *fp, Filestring_T *f</td>
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936
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940
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<pre style="margin: 0;"> <span id="LC940" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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937
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941
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<pre style="margin: 0;"> <span id="LC941" class="line" lang="c"> <span class="p">)</span> <span class="p">{</span></span>
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938
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942
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="c"> <span class="n" style="color: #333;">SAM_split_output_type</span> <span class="n" style="color: #333;">split_output</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="939" style="width: 35px; color: rgba(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="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
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<pre style="margin: 0;">+<span id="LC943" 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;">string</span><span class="p">;</span></span>
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939
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944
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<pre style="margin: 0;"> <span id="LC944" class="line" lang="c"></span>
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940
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945
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<pre style="margin: 0;"> <span id="LC945" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">split_output_root</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
941
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<td class="diff-line-num new_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
946
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<pre style="margin: 0;"> <span id="LC946" class="line" lang="c"> <span class="n" style="color: #333;">split_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_split_output</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="955" style="width: 35px; color: rgba(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">@@ -955,18 +960,24 @@ Outbuffer_lines_store (Outbuffer_lines_T this, Filestring_T *fp, Filestring_T *f</td>
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955
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nlines</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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956
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="c"> </span>
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957
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962
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<pre style="margin: 0;"> <span id="LC962" 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;">fp_failedinput</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="958" 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">
958
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<td class="diff-line-num new_line old" data-linenumber="963" 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="LC958" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">List_push</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput</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="p">)</span> <span class="n" style="color: #333;">Filestring_string</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="959" style="width: 35px; color: rgba(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="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_string</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="959" style="width: 35px; color: rgba(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="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">List_push</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput</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="p">)</span> <span class="n" style="color: #333;">string</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="c"> <span class="p">}</span></span>
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959
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<td class="diff-line-num new_line" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_free</span><span class="p">(</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;">fp_failedinput</span><span class="p">),</span><span class="cm" style="color: #998; font-style: italic;">/*free_string_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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960
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="c"> <span class="p">}</span></span>
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961
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968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="c"></span>
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962
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969
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<pre style="margin: 0;"> <span id="LC969" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef GSNAP</span></span>
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963
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<td class="diff-line-num new_line" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
970
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<pre style="margin: 0;"> <span id="LC970" 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;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="964" 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">
964
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<td class="diff-line-num new_line old" data-linenumber="971" 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="LC964" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">List_push</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput_1</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="p">)</span> <span class="n" style="color: #333;">Filestring_string</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span><span class="p">));</span></span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_string</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">List_push</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput_1</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="p">)</span> <span class="n" style="color: #333;">string</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="c"> <span class="p">}</span></span>
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965
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<td class="diff-line-num 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">
974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_free</span><span class="p">(</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;">fp_failedinput_1</span><span class="p">),</span><span class="cm" style="color: #998; font-style: italic;">/*free_string_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
966
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<td class="diff-line-num new_line" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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967
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<td class="diff-line-num new_line" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
976
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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;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="968" 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">
968
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<td class="diff-line-num new_line old" data-linenumber="977" 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="LC968" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">List_push</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput_2</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="p">)</span> <span class="n" style="color: #333;">Filestring_string</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="969" 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">
969
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<td class="diff-line-num new_line old" data-linenumber="977" 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="LC969" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_free</span><span class="p">(</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;">fp_failedinput_1</span><span class="p">),</span><span class="cm" style="color: #998; font-style: italic;">/*free_string_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="970" style="width: 35px; color: rgba(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="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_string</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">List_push</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lines_failedinput_2</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="p">)</span> <span class="n" style="color: #333;">string</span><span class="p">);</span></span>
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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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<td class="diff-line-num new new_line" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_free</span><span class="p">(</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;">fp_failedinput_2</span><span class="p">),</span><span class="cm" style="color: #998; font-style: italic;">/*free_string_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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970
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981
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<pre style="margin: 0;"> <span id="LC981" class="line" lang="c"> <span class="p">}</span></span>
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971
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<td class="diff-line-num new_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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972
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<td class="diff-line-num new_line" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
983
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC983" class="line" lang="c"></span>
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<li id="c672fce9c671440792e33117e131e53e07e9ddc6">
<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#c672fce9c671440792e33117e131e53e07e9ddc6"><strong>src/output.c</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: output.c 223<span class="idiff left right">774 2020-12-14 19:16:04</span>Z twu $"</span><span class="p">;</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: output.c 223<span class="idiff left right">811 2021-02-13 21:51:27</span>Z twu $"</span><span class="p">;</span></span>
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2
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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4
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -394,18 +394,13 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail</td>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="c"> <span class="n" style="color: #333;">Shortread_T</span> <span class="n" style="color: #333;">queryseq1</span><span class="p">,</span> <span class="n" style="color: #333;">queryseq2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="c"> <span class="n" style="color: #333;">Stage3end_T</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stage3array</span><span class="p">,</span> <span class="n" style="color: #333;">stage3</span><span class="p">;</span></span>
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396
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">npaths_primary</span><span class="p">,</span> <span class="n" style="color: #333;">npaths_altloc</span><span class="p">,</span> <span class="n" style="color: #333;">pathnum</span><span class="p">,</span> <span class="n" style="color: #333;">first_absmq</span><span class="p">,</span> <span class="n" style="color: #333;">second_absmq</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;">bool</span> <span class="n" style="color: #333;">print1p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">print2p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">single_end_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="c"> <span class="n" style="color: #333;">resulttype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Result_resulttype</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">resulttype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SINGLEEND_NOMAPPING</span><span class="p">)</span> <span class="p">{</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failedinput_root</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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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 class="k" style="font-weight: 600;">else</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 class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">));</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">resulttype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SINGLEEND_NOMAPPING</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="c"> <span class="n" style="color: #333;">single_end_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nofailsp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* No output */</span></span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Filestring_set_split_output(fp,OUTPUT_NONE); -- Already initialized to be OUTPUT_NONE */</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">@@ -416,21 +411,10 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail</td>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_NM</span><span class="p">);</span></span>
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417
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="c"> <span class="n" style="color: #333;">print_header_singleend</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">request</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*translocationp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*npaths_primary*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*npaths_altloc*/</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</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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<pre style="margin: 0;">-<span id="LC419" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failedinput_root</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="c"> <span class="n" style="color: #333;">queryseq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Request_queryseq1</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="c"> <span class="n" style="color: #333;">Shortread_print_query_singleend</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span><span class="p">,</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC416" 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;">resulttype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SINGLEEND_UNIQ</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failedinput_root</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC429" 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="LC430" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><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="LC417" class="line" lang="c"> <span class="n" style="color: #333;">single_end_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failsonlyp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Filestring_set_split_output(fp,OUTPUT_NONE); -- Already initialized to be OUTPUT_NONE */</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">@@ -441,6 +425,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail</td>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"> <span class="n" style="color: #333;">stage3array</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Stage3end_T</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">Result_array</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">npaths_primary</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">npaths_altloc</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">first_absmq</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">second_absmq</span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="c"> <span class="n" style="color: #333;">stage3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stage3array</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="LC427" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="c"> <span class="n" style="color: #333;">print1p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="c"> <span class="n" style="color: #333;">print_header_singleend</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">request</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*translocationp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="n" style="color: #333;">npaths_primary</span><span class="p">,</span><span class="n" style="color: #333;">npaths_altloc</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="c"> <span class="n" style="color: #333;">Stage3end_print</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*stage3pair*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">stage3</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="c"> <span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*acc_suffix*/</span><span class="s" style="color: #d14;">""</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">@@ -453,13 +438,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail</td>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC440" 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;">resulttype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SINGLEEND_TRANSLOC</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failedinput_root</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC458" 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="LC459" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="c"> <span class="n" style="color: #333;">single_end_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_UT</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="c"> <span class="n" style="color: #333;">stage3array</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Stage3end_T</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">Result_array</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">npaths_primary</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">npaths_altloc</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">first_absmq</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">second_absmq</span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="459" style="width: 35px; color: rgba(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">@@ -480,6 +459,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail</td>
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459
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<pre style="margin: 0;"> <span id="LC459" 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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481
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="c"> <span class="n" style="color: #333;">queryseq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Request_queryseq1</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="c"> <span class="n" style="color: #333;">print1p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="c"> <span class="n" style="color: #333;">print_header_singleend</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">request</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*translocationp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="n" style="color: #333;">npaths_primary</span><span class="p">,</span><span class="n" style="color: #333;">npaths_altloc</span><span class="p">);</span></span>
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484
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">pathnum</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;">pathnum</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">npaths_primary</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">npaths_altloc</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pathnum</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxpaths_report</span><span class="p">;</span> <span class="n" style="color: #333;">pathnum</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="c"> <span class="n" style="color: #333;">stage3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stage3array</span><span class="p">[</span><span class="n" style="color: #333;">pathnum</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 unfold js-unfold new_line" data-linenumber="475" style="width: 35px; color: rgba(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">@@ -495,13 +475,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail</td>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">resulttype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SINGLEEND_MULT</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failedinput_root</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC500" 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="LC501" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="c"> <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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</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>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="c"> <span class="n" style="color: #333;">single_end_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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505
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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;">stage3array</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Stage3end_T</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">Result_array</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">npaths_primary</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">npaths_altloc</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">first_absmq</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">second_absmq</span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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506
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480
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="c"></span>
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507
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failsonlyp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</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="523" style="width: 35px; color: rgba(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="497" style="width: 35px; color: rgba(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">@@ -523,6 +497,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail</td>
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523
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497
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<pre style="margin: 0;"> <span id="LC497" 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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524
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="c"> <span class="n" style="color: #333;">queryseq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Request_queryseq1</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">);</span></span>
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525
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="c"> <span class="n" style="color: #333;">print1p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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526
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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;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_UM</span><span class="p">);</span></span>
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527
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="c"> <span class="n" style="color: #333;">print_header_singleend</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">request</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*translocationp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="n" style="color: #333;">npaths_primary</span><span class="p">,</span><span class="n" style="color: #333;">npaths_altloc</span><span class="p">);</span></span>
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528
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">pathnum</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;">pathnum</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">npaths_primary</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">npaths_altloc</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pathnum</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxpaths_report</span><span class="p">;</span> <span class="n" style="color: #333;">pathnum</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 unfold js-unfold old_line" data-linenumber="539" style="width: 35px; color: rgba(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="514" style="width: 35px; color: rgba(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">@@ -539,15 +514,6 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail</td>
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539
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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>
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515
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="c"></span>
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541
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516
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<pre style="margin: 0;"> <span id="LC516" 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;">resulttype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIREDEND_NOMAPPING</span><span class="p">)</span> <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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failedinput_root</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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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="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nofailsp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* No output */</span></span>
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Filestring_set_split_output(fp,OUTPUT_NONE); -- Already initialized to be OUTPUT_NONE */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="557" style="width: 35px; color: rgba(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="523" style="width: 35px; color: rgba(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">@@ -557,30 +523,17 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail</td>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Stage3pair_print_end will call Filestring_set_split_output(), based on resulttype */</span></span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* First end */</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">Stage3pair_print_end</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fp</span></span><span class="p"><span class="idiff">,</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">fp_failedinput_1</span></span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">,</span><span class="n" style="color: #333;">resulttype</span><span class="p">,</span><span class="sc" style="color: #d14;">'>'</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*firstp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*queryseq*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq1*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq2*/</span><span class="n" style="color: #333;">queryseq2</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;">maxpaths_report</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span><span class="n" style="color: #333;">invert_first_p</span><span class="p">,</span><span class="n" style="color: #333;">quality_shift</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">print1p</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">Stage3pair_print_end</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fp</span></span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">,</span><span class="n" style="color: #333;">resulttype</span><span class="p">,</span><span class="sc" style="color: #d14;">'>'</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*firstp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="c"> <span class="idiff left right"> </span> <span class="cm" style="color: #998; font-style: italic;">/*queryseq*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq1*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq2*/</span><span class="n" style="color: #333;">queryseq2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="c"> <span class="idiff left right"> </span> <span class="n" style="color: #333;">maxpaths_report</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span><span class="n" style="color: #333;">invert_first_p</span><span class="p">,</span><span class="n" style="color: #333;">quality_shift</span><span class="p">);</span></span>
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="c"></span>
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564
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Second end */</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;">Stage3pair_print_end</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">,</span><span class="n" style="color: #333;">resulttype</span><span class="p">,</span><span class="sc" style="color: #d14;">'<'</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*firstp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</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="cm" style="color: #998; font-style: italic;">/*queryseq*/</span><span class="n" style="color: #333;">queryseq2</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq1*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq2*/</span><span class="n" style="color: #333;">queryseq2</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;">maxpaths_report</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span><span class="n" style="color: #333;">invert_second_p</span><span class="p">,</span><span class="n" style="color: #333;">quality_shift</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>
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569
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failedinput_root</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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570
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="c"> <span class="n" style="color: #333;">Shortread_print_query_pairedend</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">,</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="n" style="color: #333;">queryseq2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="571" 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">
571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="572" style="width: 35px; color: rgba(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="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="c"> <span class="n" style="color: #333;">print2p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Stage3pair_print_end</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">,</span><span class="n" style="color: #333;">resulttype</span><span class="p">,</span><span class="sc" style="color: #d14;">'<'</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*firstp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*queryseq*/</span><span class="n" style="color: #333;">queryseq2</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq1*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq2*/</span><span class="n" style="color: #333;">queryseq2</span><span class="p">,</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="c"> <span class="n" style="color: #333;">maxpaths_report</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span><span class="n" style="color: #333;">invert_second_p</span><span class="p">,</span><span class="n" style="color: #333;">quality_shift</span><span class="p">);</span></span>
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572
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="c"> <span class="p">}</span></span>
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573
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<td class="diff-line-num new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="c"></span>
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574
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<td class="diff-line-num new_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="575" 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">
575
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<td class="diff-line-num new_line old" data-linenumber="537" 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="LC575" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="576" 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">
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;">failedinput_root</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="577" 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">
577
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<td class="diff-line-num new_line old" data-linenumber="537" 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="LC577" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="578" 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">
578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="579" 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">
579
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<td class="diff-line-num new_line old" data-linenumber="537" 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="LC579" 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 old_line" data-linenumber="580" 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">
580
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<td class="diff-line-num new_line old" data-linenumber="537" 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="LC580" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failsonlyp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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585
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Unwanted success: skip */</span></span>
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586
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Filestring_set_split_output(fp,OUTPUT_NONE); -- Already initialized to be OUTPUT_NONE */</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">@@ -591,14 +544,44 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail</td>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Stage3pair_print_end will call Filestring_set_split_output() based on resulttype */</span></span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* First end */</span></span>
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594
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">Stage3pair_print_end</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fp</span></span><span class="p"><span class="idiff">,</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">fp_failedinput_1</span></span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">,</span><span class="n" style="color: #333;">resulttype</span><span class="p">,</span><span class="sc" style="color: #d14;">'>'</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*firstp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</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 class="cm" style="color: #998; font-style: italic;">/*queryseq*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq1*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq2*/</span><span class="n" style="color: #333;">queryseq2</span><span class="p">,</span></span>
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596
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="c"> <span class="n" style="color: #333;">maxpaths_report</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span><span class="n" style="color: #333;">invert_first_p</span><span class="p">,</span><span class="n" style="color: #333;">quality_shift</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;"><span class="idiff left">print1p</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">Stage3pair_print_end</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fp</span></span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">,</span><span class="n" style="color: #333;">resulttype</span><span class="p">,</span><span class="sc" style="color: #d14;">'>'</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*firstp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="c"> <span class="idiff left right"> </span> <span class="cm" style="color: #998; font-style: italic;">/*queryseq*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq1*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq2*/</span><span class="n" style="color: #333;">queryseq2</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="idiff left right"> </span> <span class="n" style="color: #333;">maxpaths_report</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span><span class="n" style="color: #333;">invert_first_p</span><span class="p">,</span><span class="n" style="color: #333;">quality_shift</span><span class="p">);</span></span>
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597
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550
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="c"></span>
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598
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<td class="diff-line-num new_line" data-linenumber="551" style="width: 35px; color: rgba(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="LC551" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Second end */</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;">Stage3pair_print_end</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">,</span><span class="n" style="color: #333;">resulttype</span><span class="p">,</span><span class="sc" style="color: #d14;">'<'</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*firstp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</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="cm" style="color: #998; font-style: italic;">/*queryseq*/</span><span class="n" style="color: #333;">queryseq2</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq1*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq2*/</span><span class="n" style="color: #333;">queryseq2</span><span class="p">,</span></span>
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601
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="c"> <span class="n" style="color: #333;">maxpaths_report</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span><span class="n" style="color: #333;">invert_second_p</span><span class="p">,</span><span class="n" style="color: #333;">quality_shift</span><span class="p">);</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="c"> <span class="n" style="color: #333;">print2p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Stage3pair_print_end</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">,</span><span class="n" style="color: #333;">resulttype</span><span class="p">,</span><span class="sc" style="color: #d14;">'<'</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*firstp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><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="cm" style="color: #998; font-style: italic;">/*queryseq*/</span><span class="n" style="color: #333;">queryseq2</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq1*/</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq2*/</span><span class="n" style="color: #333;">queryseq2</span><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="n" style="color: #333;">maxpaths_report</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span><span class="n" style="color: #333;">invert_second_p</span><span class="p">,</span><span class="n" style="color: #333;">quality_shift</span><span class="p">);</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="c"> <span class="p">}</span></span>
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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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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="c"></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">single_end_p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failedinput_root</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
562
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<pre style="margin: 0;">+<span id="LC562" 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;">print1p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</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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<td class="diff-line-num new new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="c"> <span class="n" style="color: #333;">queryseq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Request_queryseq1</span><span class="p">(</span><span class="n" style="color: #333;">request</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;">Shortread_print_query_singleend</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span><span class="p">,</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*headerseq1*/</span><span class="n" style="color: #333;">queryseq1</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="p">}</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
569
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<pre style="margin: 0;">+<span id="LC569" 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="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failedinput_root</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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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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<td class="diff-line-num new new_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
575
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<pre style="margin: 0;">+<span id="LC575" 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;">print1p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">print2p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</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>
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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="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Filestring_new</span><span class="p">(</span><span class="n" style="color: #333;">Request_id</span><span class="p">(</span><span class="n" style="color: #333;">request</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="n" style="color: #333;">queryseq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Request_queryseq1</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">);</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="c"> <span class="n" style="color: #333;">queryseq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Request_queryseq2</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="c"> <span class="n" style="color: #333;">Shortread_print_query_pairedend</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_1</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">,</span><span class="n" style="color: #333;">queryseq1</span><span class="p">,</span><span class="n" style="color: #333;">queryseq2</span><span class="p">);</span></span>
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602
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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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603
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586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="c"> <span class="p">}</span></span>
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604
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="c"></span>
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<li id="41c3f2188ff05d862f9f803bd84d0d1d705983fa">
<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#41c3f2188ff05d862f9f803bd84d0d1d705983fa"><strong>src/resulthr.c</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: resulthr.c 223<span class="idiff left right">349 2020-10-28 02:49:25</span>Z twu $"</span><span class="p">;</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: resulthr.c 223<span class="idiff left right">804 2021-02-13 17:17:31</span>Z twu $"</span><span class="p">;</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -297,7 +297,14 @@ Result_free (T *old) {</td>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="c"> <span class="n" style="color: #333;">Stage3pair_T</span> <span class="n" style="color: #333;">stage3pair</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">old</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">resulttype</span><span class="p">)</span> <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="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">SINGLEEND_NOMAPPING</span><span class="p">:</span> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">PAIREDEND_NOMAPPING</span><span class="p">:</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">SINGLEEND_NOMAPPING</span><span class="p">:</span> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">PAIREDEND_NOMAPPING</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* It is possible to have results that are not printed because of various flags */</span></span>
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<pre style="margin: 0;">+<span id="LC302" 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="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">old</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">npaths_primary</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;">old</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">npaths_altloc</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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<pre style="margin: 0;">+<span id="LC303" class="line" lang="c"> <span class="n" style="color: #333;">stage3</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;">old</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">array</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="c"> <span class="n" style="color: #333;">Stage3end_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stage3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="c"> <span class="n" style="color: #333;">FREE_OUT</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">old</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">array</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">SINGLEEND_UNIQ</span><span class="p">:</span> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">SINGLEEND_TRANSLOC</span><span class="p">:</span> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">SINGLEEND_MULT</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC310" 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="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">old</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">npaths_primary</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;">old</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">npaths_altloc</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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<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#2d331dd15dccff926559b191048c3a7d2d3a5fae"><strong>src/stage3hr.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="">static char rcsid[] = "$Id: stage3hr.c 223<span class="idiff left right">538 2020-11-15 12:03:08</span>Z twu $";</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="">static char rcsid[] = "$Id: stage3hr.c 223<span class="idiff left right">808 2021-02-13 18:47:25</span>Z twu $";</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="">#ifdef HAVE_CONFIG_H</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="">#include "config.h"</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="">#endif</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">@@ -5368,9 +5368,9 @@ Stage3end_new_splice (int *found_score_overall, int *found_score_within_trims,</td>
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5368
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5368
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<pre style="margin: 0;"> <span id="LC5368" class="line" lang=""> Substring_T substring1, substringN;</span>
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5369
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5369
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<pre style="margin: 0;"> <span id="LC5369" class="line" lang=""> Junction_T junction;</span>
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5370
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5370
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<pre style="margin: 0;"> <span id="LC5370" class="line" lang=""></span>
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5371
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<pre style="margin: 0;">-<span id="LC5371" class="line" lang=""> <span class="idiff left right">List_T transcripts;</span></span>
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5372
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<pre style="margin: 0;">-<span id="LC5372" class="line" lang=""> <span class="idiff left right">char *remap_sequence;</span></span>
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5373
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<pre style="margin: 0;">-<span id="LC5373" class="line" lang=""> <span class="idiff left right">int remap_seqlength;</span></span>
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<pre style="margin: 0;">+<span id="LC5371" class="line" lang=""> <span class="idiff left right">/* List_T transcripts; */</span></span>
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<pre style="margin: 0;">+<span id="LC5372" class="line" lang=""> <span class="idiff left right">/* char *remap_sequence; */</span></span>
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<pre style="margin: 0;">+<span id="LC5373" class="line" lang=""> <span class="idiff left right">/* int remap_seqlength; */</span></span>
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<pre style="margin: 0;"> <span id="LC5374" class="line" lang=""> double donor_prob, acceptor_prob;</span>
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<pre style="margin: 0;"> <span id="LC5375" class="line" lang="">#ifdef DEBUG0</span>
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5376
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<pre style="margin: 0;"> <span id="LC5376" class="line" lang=""> Substring_T substring;</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">@@ -5706,9 +5706,9 @@ Stage3end_new_distant (int *found_score_overall, int *found_score_within_trims,</td>
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5706
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5706
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<pre style="margin: 0;"> <span id="LC5706" class="line" lang=""> Substring_T donor, acceptor;</span>
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5707
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<pre style="margin: 0;"> <span id="LC5707" class="line" lang=""> Junction_T junction;</span>
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<pre style="margin: 0;"> <span id="LC5708" class="line" lang=""></span>
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5709
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<pre style="margin: 0;">-<span id="LC5709" class="line" lang=""> <span class="idiff left right">List_T transcripts;</span></span>
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5710
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<pre style="margin: 0;">-<span id="LC5710" class="line" lang=""> <span class="idiff left right">char *remap_sequence;</span></span>
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5711
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<pre style="margin: 0;">-<span id="LC5711" class="line" lang=""> <span class="idiff left right">int remap_seqlength;</span></span>
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<pre style="margin: 0;">+<span id="LC5709" class="line" lang=""> <span class="idiff left right">/* List_T transcripts; */</span></span>
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<pre style="margin: 0;">+<span id="LC5710" class="line" lang=""> <span class="idiff left right">/* char *remap_sequence; */</span></span>
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<pre style="margin: 0;">+<span id="LC5711" class="line" lang=""> <span class="idiff left right">/* int remap_seqlength; */</span></span>
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<pre style="margin: 0;"> <span id="LC5712" class="line" lang="">#ifdef DEBUG0</span>
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5713
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5713
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<pre style="margin: 0;"> <span id="LC5713" class="line" lang=""> Substring_T substring;</span>
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5714
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5714
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<pre style="margin: 0;"> <span id="LC5714" class="line" lang=""> List_T p;</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">@@ -10074,18 +10074,17 @@ print_barcode_and_quality (Filestring_T fp, Shortread_T queryseq, bool invertp,</td>
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10074
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10074
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<pre style="margin: 0;"> <span id="LC10074" class="line" lang="">}</span>
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10075
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10075
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<pre style="margin: 0;"> <span id="LC10075" class="line" lang=""></span>
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10076
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10076
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<pre style="margin: 0;"> <span id="LC10076" class="line" lang=""></span>
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10077
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<pre style="margin: 0;">-<span id="LC10077" class="line" lang="">void</span>
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10078
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<pre style="margin: 0;">-<span id="LC10078" class="line" lang="">Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</span>
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10079
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<pre style="margin: 0;">-<span id="LC10079" class="line" lang=""> Result_T result, Resulttype_T resulttype,</span>
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10077
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<pre style="margin: 0;">+<span id="LC10077" class="line" lang="">bool</span>
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10078
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<pre style="margin: 0;">+<span id="LC10078" class="line" lang="">Stage3pair_print_end (Filestring_T fp, Result_T result, Resulttype_T resulttype,</span>
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10080
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10079
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<pre style="margin: 0;"> <span id="LC10079" class="line" lang=""> char initchar, bool firstp, Univ_IIT_T chromosome_iit,</span>
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10081
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10080
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<pre style="margin: 0;"> <span id="LC10080" class="line" lang=""> Shortread_T queryseq, Shortread_T headerseq1, Shortread_T headerseq2,</span>
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10082
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10081
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<pre style="margin: 0;"> <span id="LC10081" class="line" lang=""> int maxpaths, bool quiet_if_excessive_p,</span>
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10083
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10082
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<pre style="margin: 0;"> <span id="LC10082" class="line" lang=""> bool invertp, int quality_shift) {</span>
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10083
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<pre style="margin: 0;">+<span id="LC10083" class="line" lang=""> bool printp = false, excessivep, translocationp;</span>
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10084
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10084
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<pre style="margin: 0;"> <span id="LC10084" class="line" lang=""> Stage3pair_T *stage3pairarray, stage3pair;</span>
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10085
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10085
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<pre style="margin: 0;"> <span id="LC10085" class="line" lang=""> T *stage3array, *stage3array_mate, this, hit5, hit3;</span>
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10086
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10086
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<pre style="margin: 0;"> <span id="LC10086" class="line" lang=""> int npaths_primary, npaths_altloc, npaths_mate_primary, npaths_mate_altloc, pathnum;</span>
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10087
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10087
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<pre style="margin: 0;"> <span id="LC10087" class="line" lang=""> int first_absmq, second_absmq;</span>
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10088
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<pre style="margin: 0;">-<span id="LC10088" class="line" lang=""> bool excessivep, translocationp;</span>
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10089
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10088
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<pre style="margin: 0;"> <span id="LC10088" class="line" lang=""></span>
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10090
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10089
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<pre style="margin: 0;"> <span id="LC10089" class="line" lang=""> if (resulttype == PAIREDEND_NOMAPPING) {</span>
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10091
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10090
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<pre style="margin: 0;"> <span id="LC10090" class="line" lang=""> if (output_type != M8_OUTPUT) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10099" style="width: 35px; color: rgba(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="10098" style="width: 35px; color: rgba(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">@@ -10099,7 +10098,6 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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10099
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10098
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<pre style="margin: 0;"> <span id="LC10098" class="line" lang=""> Shortread_print_header(fp,headerseq1,headerseq2);</span>
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10099
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<pre style="margin: 0;"> <span id="LC10099" class="line" lang=""> FPRINTF(fp,"\n");</span>
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<td class="diff-line-num old_line" data-linenumber="10101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10101
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10100
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<pre style="margin: 0;"> <span id="LC10100" class="line" lang=""> }</span>
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10102
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<td class="diff-line-num new_line old" data-linenumber="10101" 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="LC10102" class="line" lang=""> /* If failedinput_root != NULL, then this case is handled by calling procedure */</span>
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<td class="diff-line-num old_line" data-linenumber="10103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10103
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10101
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<pre style="margin: 0;"> <span id="LC10101" class="line" lang=""></span>
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<td class="diff-line-num old_line" data-linenumber="10104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10104
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10102
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<pre style="margin: 0;"> <span id="LC10102" class="line" lang=""> } else if (resulttype == CONCORDANT_UNIQ) {</span>
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<td class="diff-line-num old_line" data-linenumber="10105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10105
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<td class="diff-line-num new_line" data-linenumber="10103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10103
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<pre style="margin: 0;"> <span id="LC10103" class="line" lang=""> stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10128" style="width: 35px; color: rgba(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="10126" style="width: 35px; color: rgba(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">@@ -10128,6 +10126,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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<td class="diff-line-num old_line" data-linenumber="10128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10128
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<td class="diff-line-num new_line" data-linenumber="10126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10126
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<pre style="margin: 0;"> <span id="LC10126" class="line" lang=""> Shortread_print_header(fp,headerseq1,headerseq2);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10129
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<td class="diff-line-num new_line" data-linenumber="10127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10127
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<pre style="margin: 0;"> <span id="LC10127" class="line" lang=""> }</span>
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<td class="diff-line-num old_line" data-linenumber="10130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10130
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10128
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<pre style="margin: 0;"> <span id="LC10128" class="line" lang=""> </span>
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<td class="diff-line-num new old_line" data-linenumber="10131" style="width: 35px; color: rgba(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="10129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10129
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<pre style="margin: 0;">+<span id="LC10129" class="line" lang=""> printp = true;</span>
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10131
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<td class="diff-line-num new_line" data-linenumber="10130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10130
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<pre style="margin: 0;"> <span id="LC10130" class="line" lang=""> if (firstp == true) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10132
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10131
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<pre style="margin: 0;"> <span id="LC10131" class="line" lang=""> Stage3end_print(fp,stage3pair,hit5,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10133
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10132
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<pre style="margin: 0;"> <span id="LC10132" class="line" lang=""> chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10171" style="width: 35px; color: rgba(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="10170" style="width: 35px; color: rgba(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">@@ -10171,10 +10170,6 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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<td class="diff-line-num old_line" data-linenumber="10171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10171
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10170
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<pre style="margin: 0;"> <span id="LC10170" class="line" lang=""> FPRINTF(fp,"\n");</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10172
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10171
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<pre style="margin: 0;"> <span id="LC10171" class="line" lang=""> }</span>
</pre>
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10173
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10172
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<pre style="margin: 0;"> <span id="LC10172" class="line" lang=""></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10174" 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">
10174
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<td class="diff-line-num new_line old" data-linenumber="10173" 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="LC10174" class="line" lang=""> if (failedinput_root != NULL) {</span>
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<td class="diff-line-num old old_line" data-linenumber="10175" 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">
10175
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<td class="diff-line-num new_line old" data-linenumber="10173" 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="LC10175" class="line" lang=""> Shortread_print_query_singleend(fp_failedinput,queryseq,headerseq1);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10176" 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">
10176
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<td class="diff-line-num new_line old" data-linenumber="10173" 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="LC10176" class="line" lang=""> }</span>
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<td class="diff-line-num old old_line" data-linenumber="10177" 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">
10177
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<pre style="margin: 0;">-<span id="LC10177" class="line" lang=""></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10178
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10173
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<pre style="margin: 0;"> <span id="LC10173" class="line" lang=""> } else {</span>
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<td class="diff-line-num old_line" data-linenumber="10179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10179
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10174
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<pre style="margin: 0;"> <span id="LC10174" class="line" lang=""> if (output_type != M8_OUTPUT) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10180
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10175
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<pre style="margin: 0;"> <span id="LC10175" class="line" lang=""> print_query_header(fp,initchar,queryseq,invertp);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10187" style="width: 35px; color: rgba(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="10182" style="width: 35px; color: rgba(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">@@ -10187,6 +10182,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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<td class="diff-line-num old_line" data-linenumber="10187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10187
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<td class="diff-line-num new_line" data-linenumber="10182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10182
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<pre style="margin: 0;"> <span id="LC10182" class="line" lang=""> Shortread_print_header(fp,headerseq1,headerseq2);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10188
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<td class="diff-line-num new_line" data-linenumber="10183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10183
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<pre style="margin: 0;"> <span id="LC10183" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10189
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<td class="diff-line-num new_line" data-linenumber="10184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10184
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10184" class="line" lang=""></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10190" style="width: 35px; color: rgba(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="10185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10185
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<pre style="margin: 0;">+<span id="LC10185" class="line" lang=""> printp = true;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10190
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<td class="diff-line-num new_line" data-linenumber="10186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10186
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<pre style="margin: 0;"> <span id="LC10186" class="line" lang=""> for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10191
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<td class="diff-line-num new_line" data-linenumber="10187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10187
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<pre style="margin: 0;"> <span id="LC10187" class="line" lang=""> stage3pair = stage3pairarray[pathnum-1];</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10192
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<td class="diff-line-num new_line" data-linenumber="10188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10188
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<pre style="margin: 0;"> <span id="LC10188" class="line" lang=""> hit5 = stage3pair->hit5;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10237" style="width: 35px; color: rgba(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="10233" style="width: 35px; color: rgba(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">@@ -10237,10 +10233,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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<td class="diff-line-num old_line" data-linenumber="10237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10237
</td>
<td class="diff-line-num new_line" data-linenumber="10233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10233
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10233" class="line" lang=""></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10238
</td>
<td class="diff-line-num new_line" data-linenumber="10234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10234
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10234" class="line" lang=""> /* No further output */</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10239
</td>
<td class="diff-line-num new_line" data-linenumber="10235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10235
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10235" class="line" lang=""> FPRINTF(fp,"\n");</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10240" 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">
10240
</td>
<td class="diff-line-num new_line old" data-linenumber="10236" 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="LC10240" class="line" lang=""> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10241" 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">
10241
</td>
<td class="diff-line-num new_line old" data-linenumber="10236" 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="LC10241" class="line" lang=""> if (failedinput_root != NULL) {</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10242" 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">
10242
</td>
<td class="diff-line-num new_line old" data-linenumber="10236" 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="LC10242" class="line" lang=""> Shortread_print_query_singleend(fp_failedinput,queryseq,headerseq1);</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="10243" 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">
10243
</td>
<td class="diff-line-num new_line old" data-linenumber="10236" 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="LC10243" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10244" style="width: 35px; color: rgba(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="10236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10236
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<pre style="margin: 0;">+<span id="LC10236" class="line" lang=""> printp = false;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10244
</td>
<td class="diff-line-num new_line" data-linenumber="10237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10237
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10237" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10245
</td>
<td class="diff-line-num new_line" data-linenumber="10238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10238
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10238" class="line" lang=""></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10246
</td>
<td class="diff-line-num new_line" data-linenumber="10239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10239
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10239" class="line" lang=""> } else {</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10255" style="width: 35px; color: rgba(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="10248" style="width: 35px; color: rgba(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">@@ -10255,6 +10248,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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<td class="diff-line-num old_line" data-linenumber="10255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10255
</td>
<td class="diff-line-num new_line" data-linenumber="10248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10248
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10248" class="line" lang=""> Shortread_print_header(fp,headerseq1,headerseq2);</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10256
</td>
<td class="diff-line-num new_line" data-linenumber="10249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10249
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10249" class="line" lang=""> }</span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10257
</td>
<td class="diff-line-num new_line" data-linenumber="10250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10250
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10250" class="line" lang=""></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="10258" style="width: 35px; color: rgba(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="10251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10251
</td>
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<pre style="margin: 0;">+<span id="LC10251" class="line" lang=""> printp = true;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10258
</td>
<td class="diff-line-num new_line" data-linenumber="10252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10252
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10252" class="line" lang=""> for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10259
</td>
<td class="diff-line-num new_line" data-linenumber="10253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10253
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10253" class="line" lang=""> stage3pair = stage3pairarray[pathnum-1];</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10260
</td>
<td class="diff-line-num new_line" data-linenumber="10254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10254
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10254" class="line" lang=""> hit5 = stage3pair->hit5;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10314" style="width: 35px; color: rgba(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="10308" style="width: 35px; color: rgba(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">@@ -10314,6 +10308,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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<td class="diff-line-num old_line" data-linenumber="10314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10314
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<td class="diff-line-num new_line" data-linenumber="10308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10308
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<pre style="margin: 0;"> <span id="LC10308" class="line" lang=""> hit5 = stage3pair->hit5;</span>
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<td class="diff-line-num old_line" data-linenumber="10315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10315
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<td class="diff-line-num new_line" data-linenumber="10309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10309
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<pre style="margin: 0;"> <span id="LC10309" class="line" lang=""> hit3 = stage3pair->hit3;</span>
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<td class="diff-line-num old_line" data-linenumber="10316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10316
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<td class="diff-line-num new_line" data-linenumber="10310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10310
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<pre style="margin: 0;"> <span id="LC10310" class="line" lang=""> </span>
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<td class="diff-line-num new old_line" data-linenumber="10317" style="width: 35px; color: rgba(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="10311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10311
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<pre style="margin: 0;">+<span id="LC10311" class="line" lang=""> printp = true;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10317
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<td class="diff-line-num new_line" data-linenumber="10312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10312
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<pre style="margin: 0;"> <span id="LC10312" class="line" lang=""> if (firstp == true) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10318
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<td class="diff-line-num new_line" data-linenumber="10313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10313
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<pre style="margin: 0;"> <span id="LC10313" class="line" lang=""> Stage3end_print(fp,stage3pair,hit5,</span>
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<td class="diff-line-num old_line" data-linenumber="10319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10319
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<td class="diff-line-num new_line" data-linenumber="10314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10314
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<pre style="margin: 0;"> <span id="LC10314" class="line" lang=""> chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10352" style="width: 35px; color: rgba(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="10347" style="width: 35px; color: rgba(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">@@ -10352,10 +10347,6 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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10352
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<td class="diff-line-num new_line" data-linenumber="10347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10347
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<pre style="margin: 0;"> <span id="LC10347" class="line" lang=""></span>
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<td class="diff-line-num old_line" data-linenumber="10353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10353
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<td class="diff-line-num new_line" data-linenumber="10348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10348
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<pre style="margin: 0;"> <span id="LC10348" class="line" lang=""> /* No further output */</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10354
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<td class="diff-line-num new_line" data-linenumber="10349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10349
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<pre style="margin: 0;"> <span id="LC10349" class="line" lang=""> FPRINTF(fp,"\n");</span>
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<td class="diff-line-num old old_line" data-linenumber="10355" 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">
10355
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<td class="diff-line-num new_line old" data-linenumber="10350" 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="LC10355" class="line" lang=""></span>
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<td class="diff-line-num old old_line" data-linenumber="10356" 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">
10356
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<td class="diff-line-num new_line old" data-linenumber="10350" 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="LC10356" class="line" lang=""> if (failedinput_root != NULL) {</span>
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<td class="diff-line-num old old_line" data-linenumber="10357" 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">
10357
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<td class="diff-line-num new_line old" data-linenumber="10350" 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="LC10357" class="line" lang=""> Shortread_print_query_singleend(fp_failedinput,queryseq,headerseq1);</span>
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<td class="diff-line-num old old_line" data-linenumber="10358" 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">
10358
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<td class="diff-line-num new_line old" data-linenumber="10350" 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="LC10358" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10359
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<td class="diff-line-num new_line" data-linenumber="10350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10350
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10350" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10360
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<td class="diff-line-num new_line" data-linenumber="10351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10351
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10351" class="line" lang=""></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10361
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<td class="diff-line-num new_line" data-linenumber="10352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10352
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<pre style="margin: 0;"> <span id="LC10352" class="line" lang=""> } else {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10370" style="width: 35px; color: rgba(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="10361" style="width: 35px; color: rgba(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">@@ -10370,6 +10361,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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<td class="diff-line-num old_line" data-linenumber="10370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10370
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<td class="diff-line-num new_line" data-linenumber="10361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10361
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10361" class="line" lang=""> Shortread_print_header(fp,headerseq1,headerseq2);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10371
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<td class="diff-line-num new_line" data-linenumber="10362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10362
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10362" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10372
</td>
<td class="diff-line-num new_line" data-linenumber="10363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10363
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10363" class="line" lang=""></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10373" style="width: 35px; color: rgba(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="10364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10364
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<pre style="margin: 0;">+<span id="LC10364" class="line" lang=""> printp = true;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10373
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<td class="diff-line-num new_line" data-linenumber="10365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10365
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<pre style="margin: 0;"> <span id="LC10365" class="line" lang=""> for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10374
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<td class="diff-line-num new_line" data-linenumber="10366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10366
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<pre style="margin: 0;"> <span id="LC10366" class="line" lang=""> stage3pair = stage3pairarray[pathnum-1];</span>
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10375
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<td class="diff-line-num new_line" data-linenumber="10367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10367
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<pre style="margin: 0;"> <span id="LC10367" class="line" lang=""> hit5 = stage3pair->hit5;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10476" style="width: 35px; color: rgba(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="10468" style="width: 35px; color: rgba(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">@@ -10476,11 +10468,9 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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10476
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<td class="diff-line-num new_line" data-linenumber="10468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10468
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<pre style="margin: 0;"> <span id="LC10468" class="line" lang=""></span>
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<td class="diff-line-num old_line" data-linenumber="10477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10477
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<td class="diff-line-num new_line" data-linenumber="10469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10469
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<pre style="margin: 0;"> <span id="LC10469" class="line" lang=""> if (excessivep == true) {</span>
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<td class="diff-line-num old_line" data-linenumber="10478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10478
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<td class="diff-line-num new_line" data-linenumber="10470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10470
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<pre style="margin: 0;"> <span id="LC10470" class="line" lang=""> /* No output */</span>
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<td class="diff-line-num old old_line" data-linenumber="10479" 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">
10479
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<td class="diff-line-num new_line old" data-linenumber="10471" 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="LC10479" class="line" lang=""> if (failedinput_root != NULL) {</span>
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<td class="diff-line-num old old_line" data-linenumber="10480" 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">
10480
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<td class="diff-line-num new_line old" data-linenumber="10471" 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="LC10480" class="line" lang=""> Shortread_print_query_singleend(fp_failedinput,queryseq,headerseq1);</span>
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<td class="diff-line-num old old_line" data-linenumber="10481" 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">
10481
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<td class="diff-line-num new_line old" data-linenumber="10471" 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="LC10481" class="line" lang=""> }</span>
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<td class="diff-line-num old_line" data-linenumber="10482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10482
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<td class="diff-line-num new_line" data-linenumber="10471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10471
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<pre style="margin: 0;"> <span id="LC10471" class="line" lang=""> </span>
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<td class="diff-line-num old_line" data-linenumber="10483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10483
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<td class="diff-line-num new_line" data-linenumber="10472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10472
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<pre style="margin: 0;"> <span id="LC10472" class="line" lang=""> } else {</span>
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<td class="diff-line-num new new_line" data-linenumber="10473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10473
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<pre style="margin: 0;">+<span id="LC10473" class="line" lang=""> printp = true;</span>
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10484
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10474
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<pre style="margin: 0;"> <span id="LC10474" class="line" lang=""> if (firstp == true) {</span>
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<td class="diff-line-num old_line" data-linenumber="10485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10485
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<td class="diff-line-num new_line" data-linenumber="10475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10475
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<pre style="margin: 0;"> <span id="LC10475" class="line" lang=""> for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {</span>
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<td class="diff-line-num old_line" data-linenumber="10486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10486
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<td class="diff-line-num new_line" data-linenumber="10476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10476
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<pre style="margin: 0;"> <span id="LC10476" class="line" lang=""> this = stage3array[pathnum-1];</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10507" style="width: 35px; color: rgba(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="10497" style="width: 35px; color: rgba(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">@@ -10507,7 +10497,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,</td>
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10507
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10497
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<pre style="margin: 0;"> <span id="LC10497" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10508
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<td class="diff-line-num new_line" data-linenumber="10498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10498
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<pre style="margin: 0;"> <span id="LC10498" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10509
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<td class="diff-line-num new_line" data-linenumber="10499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10499
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10499" class="line" lang=""></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10510" 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">
10510
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<td class="diff-line-num new_line old" data-linenumber="10500" 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="LC10510" class="line" lang=""> return;</span>
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<td class="diff-line-num new old_line" data-linenumber="10511" style="width: 35px; color: rgba(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="10500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10500
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<pre style="margin: 0;">+<span id="LC10500" class="line" lang=""> return<span class="idiff left right"> printp</span>;</span>
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<td class="diff-line-num old_line" data-linenumber="10511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10511
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10501
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<pre style="margin: 0;"> <span id="LC10501" class="line" lang="">}</span>
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<td class="diff-line-num old_line" data-linenumber="10512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10512
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<td class="diff-line-num new_line" data-linenumber="10502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10502
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<pre style="margin: 0;"> <span id="LC10502" class="line" lang=""></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10513
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<td class="diff-line-num new_line" data-linenumber="10503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10503
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<pre style="margin: 0;"> <span id="LC10503" class="line" lang=""></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11433" style="width: 35px; color: rgba(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="11423" style="width: 35px; color: rgba(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">@@ -11433,9 +11423,9 @@ Stage3pair_new (T hit5_orig, T hit3_orig, int genestrand, int sensedir, Pairtype</td>
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<td class="diff-line-num old_line" data-linenumber="11433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11433
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11423
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<pre style="margin: 0;"> <span id="LC11423" class="line" lang=""> int querylength5 = hit5_orig->querylength;</span>
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<td class="diff-line-num old_line" data-linenumber="11434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11434
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<td class="diff-line-num new_line" data-linenumber="11424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11424
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<pre style="margin: 0;"> <span id="LC11424" class="line" lang=""> int querylength3 = hit3_orig->querylength;</span>
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<td class="diff-line-num old_line" data-linenumber="11435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11435
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<td class="diff-line-num new_line" data-linenumber="11425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11425
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<pre style="margin: 0;"> <span id="LC11425" class="line" lang=""></span>
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<pre style="margin: 0;">-<span id="LC11436" class="line" lang=""> <span class="idiff left right">char *remap_sequence;</span></span>
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11437
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<pre style="margin: 0;">-<span id="LC11437" class="line" lang=""> <span class="idiff left right">int remap_seqlength;</span></span>
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11438
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<pre style="margin: 0;">-<span id="LC11438" class="line" lang=""> <span class="idiff left right">List_T transcripts;</span></span>
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<pre style="margin: 0;">+<span id="LC11426" class="line" lang=""> <span class="idiff left right">/* char *remap_sequence; */</span></span>
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<pre style="margin: 0;">+<span id="LC11427" class="line" lang=""> <span class="idiff left right">/* int remap_seqlength; */</span></span>
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<pre style="margin: 0;">+<span id="LC11428" class="line" lang=""> <span class="idiff left right">/* List_T transcripts; */</span></span>
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11429
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<pre style="margin: 0;"> <span id="LC11429" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC11430" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC11431" class="line" lang=""> debug0(printf("\nStage3pair_new called with pairtype %s and chrnum %d, %d (effective %d, %d), expect_concordant_p %d\n",</span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/10b06cba91d10f5c5f5beccaa75e359cd4728de3...a691ebb5eaead2f6c2cb8d9ee771c6f03cfc28af#1f55d42fa4aff8ae5015454067ccb1a098a3964e"><strong>src/stage3hr.h</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* $Id: stage3hr.h 223<span class="idiff left right">538 2020-11-15 12:03:08</span>Z twu $ */</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* $Id: stage3hr.h 223<span class="idiff left right">808 2021-02-13 18:47:25</span>Z twu $ */</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef STAGE3HR_INCLUDED</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define STAGE3HR_INCLUDED</span></span>
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<pre style="margin: 0;"> <span id="LC4" 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">@@ -420,9 +420,8 @@ Stage3end_print_transcript_info (Filestring_T fp, Intlist_T trnums, Intlist_T tr</td>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Stage3end_print_transcript_diff</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">hit</span><span class="p">,</span> <span class="n" style="color: #333;">Intlist_T</span> <span class="n" style="color: #333;">common_trnums</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">invertp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Stage3pair_print_end</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">Filestring_T</span> <span class="n" style="color: #333;">fp_failedinput</span><span class="p">,</span></span>
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425
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="c"> <span class="n" style="color: #333;">Result_T</span> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">Resulttype_T</span> <span class="n" style="color: #333;">resulttype</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;">extern</span> <span class="n" style="color: #333;">bool</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Stage3pair_print_end</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">Result_T</span> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">Resulttype_T</span> <span class="n" style="color: #333;">resulttype</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">initchar</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">firstp</span><span class="p">,</span> <span class="n" style="color: #333;">Univ_IIT_T</span> <span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="c"> <span class="n" style="color: #333;">Shortread_T</span> <span class="n" style="color: #333;">queryseq</span><span class="p">,</span> <span class="n" style="color: #333;">Shortread_T</span> <span class="n" style="color: #333;">headerseq1</span><span class="p">,</span> <span class="n" style="color: #333;">Shortread_T</span> <span class="n" style="color: #333;">headerseq2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxpaths</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span></span>
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