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GitLab

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<h3>

Steffen Möller pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/7cf8a32fe5714675dba5039399800a5d74c41c09">7cf8a32f</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:28:17+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Improving clean, removing 'mutable' file from source

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/962d0f02962fac3d1a6cf169ef0fb910a7122f69">962d0f02</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:29:58+02:00</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/subread/-/commit/581d5ef26ce8e53c4a026feb096ee98e2510aec4">581d5ef2</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:30:00+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.1+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/e156e623e61804cda68677206c083550482fa802">e156e623</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:31:05+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.0.1+dfsg'

Update to upstream version '2.0.1+dfsg'

with Debian dir df644a12f73b9540258721b5e7224f10e816d080</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/2fe4255060a4e758604e3a7fb06f880da94f588e">2fe42550</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:31:05+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/b9ecda15ebe3afc3d2c60c8875b64d5a1d25476b">b9ecda15</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:31:07+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/0aecd04ad979a82588190c34c93e5024557b19eb">0aecd04a</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:31:08+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/5ec87e7f13d088b61348664153de452be94f756e">5ec87e7f</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:31:19+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Archive.</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/42bce8912699a3696f5f35a8cd1981c00e15ac45">42bce891</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:31:20+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rely on pre-initialized dpkg-architecture variables.

Fixes: lintian: debian-rules-sets-dpkg-architecture-variable

See-also: https://lintian.debian.org/tags/debian-rules-sets-dpkg-architecture-variable.html

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/d1aa4a7ec9b294ff1b5ccb366122fe1d8be2d54b">d1aa4a7e</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:34:47+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/779708682bfd2bfcd7811a9c27a8e500e8f81630">77970868</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-05-22T19:56:14+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cosmetics prior to upload

</pre>

</li>

</ul>

<h4>28 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

debian/copyright

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

<li class="file-stats">

<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">

<span class="new-file">

+

debian/salsa-ci.yml

</span>

</a>

</li>

<li class="file-stats">

<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">

debian/upstream/metadata

</a>

</li>

<li class="file-stats">

<a href="#9b9715372d0cd39d21711a077b6f2ae42fb45135">

doc/SubreadUsersGuide.tex

</a>

</li>

<li class="file-stats">

<a href="#7079f81404dcaadc0154c53a419b2d1cb5f253e6">

src/HelperFunctions.c

</a>

</li>

<li class="file-stats">

<a href="#ecc92c74c51f8b1692fd1bd13b9657e456522c0a">

src/core-interface-aligner.c

</a>

</li>

<li class="file-stats">

<a href="#d7c9610d0bb39f36045810aea42dfc930a2d041f">

src/core-junction.c

</a>

</li>

<li class="file-stats">

<a href="#a26ea438a2b6aee04f419d17c87da7e9b997e7ae">

src/core.c

</a>

</li>

<li class="file-stats">

<a href="#3ff152fe6bda3f5dfee9715abff394de66921551">

src/core.h

</a>

</li>

<li class="file-stats">

<a href="#08ec1eca3761439e06c59fe3179a2eb515dfacb1">

src/detection-calls.c

</a>

</li>

<li class="file-stats">

<a href="#69742224d661e373a40a3e0ffe96a88520f33874">

src/flattenAnnotations.c

</a>

</li>

<li class="file-stats">

<a href="#18d5c843fdde01c811087dacdcf7dbe1f38af4d3">

src/gene-algorithms.c

</a>

</li>

<li class="file-stats">

<a href="#6612baeecf620e30ab51b9fb8e8a2afe1d40812b">

src/hashtable.c

</a>

</li>

<li class="file-stats">

<a href="#30c07b024c4fcae2a43837631bde802ba5d8e371">

src/hashtable.h

</a>

</li>

<li class="file-stats">

<a href="#db883abc086707d455e41cc6745055f2475bcc7f">

src/index-builder.c

</a>

</li>

<li class="file-stats">

<a href="#af240e90f84ee342e36f1a8ee0eb08f1a4b16a3d">

src/input-files.c

</a>

</li>

<li class="file-stats">

<a href="#6907133cceb8c785482dac4a3125dbff95a3d8e2">

src/input-files.h

</a>

</li>

<li class="file-stats">

<a href="#76cc7b82fd823387133c6778766e61c15828100c">

src/makefile.version

</a>

</li>

<li class="file-stats">

<a href="#2ec8748eb117e101c7a40d2a3e3c5d8cf22f9dd9">

src/readSummary.c

</a>

</li>

<li class="file-stats">

<a href="#f86ff9b8aeda4b6603bb5a33b2b3a6251be1c2e9">

src/sambam-file.c

</a>

</li>

<li class="file-stats">

<a href="#03fc71344ae0dba380c866ea91a52d0334a86e42">

src/sorted-hashtable.c

</a>

</li>

<li class="file-stats">

<a href="#8668314c149b82a2621dd7e1430711059f36c080">

src/subread.h

</a>

</li>

<li class="file-stats">

<a href="#6eea7570e32aaa0baae17b9c4acbe8539b60b3e5">

src/tx-unique.c

</a>

</li>

<li class="file-stats">

<a href="#ade6b65ee73b2ea6dede4962f8758d6e527b53f8">

<span class="deleted-file">

−

test/subread-align/data/test-err-mut-r1.fq.gz

</span>

</a>

</li>

<li class="file-stats">

<a href="#37b6cc293a92c15848e43cc61941f024afa60f9b">

<span class="deleted-file">

−

test/subread-align/data/test-err-mut-r2.fq.gz

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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

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

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

1

</td>

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">subread (2.0.1+dfsg-1) unstable; urgency=medium</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(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="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(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="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Team upload.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(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="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

</tr>

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

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

5

</td>

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Standards-Version: 4.5.0 (routine-update)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(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="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Add salsa-ci file (routine-update)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Rules-Requires-Root: no (routine-update)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">  * Set upstream metadata fields: Archive. (routine-update)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(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="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  * Rely on pre-initialized dpkg-architecture variables. (routine-update)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">  * d/rules: extended clean to allow consecutive builds</span>

</pre>

</td>

</tr>

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

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">  * d/copyright: excluded changing test/*gz files from source tree</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org>  Fri, 22 May 2020 19:31:20 +0200</span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">subread (2.0.0+dfsg-2) unstable; urgency=medium</span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">  * Add patch to build with gcc-10</span>

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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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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">@@ -10,10 +10,11 @@ Build-Depends: bc,</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               help2man,</span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">               python3,</span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">               zlib1g-dev</span>

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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5</span>.0</span>

</pre>

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14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/subread</span>

</pre>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/subread.git</span>

</pre>

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16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: http://sourceforge.net/projects/subread/</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Rules-Requires-Root: no</span>

</pre>

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17

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>

</pre>

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

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

</pre>

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

19

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: amd64 arm64 armel armhf i386 kfreebsd-amd64 kfreebsd-i386 ppc64el</span>

</pre>

</td>

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<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,8 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</td>

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<td class="diff-line-num old_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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<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">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: http://sourceforge.net/projects/subread/files/</span>

</pre>

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<td class="diff-line-num old_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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<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="plaintext">Files-Excluded: doc/*.pdf</span>

</pre>

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> test/subread-align/data/test-err-mut-r1.fq.gz</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5" style="width: 35px; color: rgba(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="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> test/subread-align/data/test-err-mut-r2.fq.gz</span>

</pre>

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

5

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Copyright: 2011-2018, Dr Yang Liao, Dr Wei Shi</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(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="13" style="width: 35px; color: rgba(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">@@ -13,7 +13,6 @@ ifeq ($(origin CC),default)</td>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(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="LC13" class="line" lang="plaintext">    CC = $(DEB_HOST_GNU_TYPE)-gcc</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(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="LC14" class="line" lang="plaintext">endif</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num new_line old" data-linenumber="16" 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="LC16" class="line" lang="plaintext">DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)</span>

</pre>

</td>

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

17

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(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="LC16" class="line" lang="plaintext">ifeq ($(DEB_HOST_ARCH),$(filter $(DEB_HOST_ARCH),amd64 i386))</span>

</pre>

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

18

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">        CFLAGS += -mtune=generic -msse3</span>

</pre>

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

19

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">endif</span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +27,12 @@ override_dh_clean:</td>

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

28

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">     cd src; make -f Makefile.Linux clean</span>

</pre>

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

29

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

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

</pre>

</td>

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

30

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

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

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">override_dh_auto_clean:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">     dh_auto_clean</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">     rm -f test/subread-align/data/test-err-mut-r1.fq.gz test/subread-align/data/test-err-mut-r2.fq.gz</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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

<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">     rm -rf bin src/longread-one/make.version</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(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="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">     find . -name "*.o" -delete</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(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="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>

</pre>

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

31

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

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">override_dh_auto_build:</span>

</pre>

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

32

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">     cd src; make -f Makefile.Linux</span>

</pre>

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

33

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">     dh_auto_build -- CC=$(CC)</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="b1dbf22e88351ec0d5d1d1a7f53295504b480e61">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>

<hr>

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</td>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>

<hr>

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</td>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Archive: SourceForge</span>

</pre>

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1

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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="plaintext">Registry:</span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> - Name: OMICtools</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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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">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">   Entry: OMICS_01255</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9b9715372d0cd39d21711a077b6f2ae42fb45135">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#9b9715372d0cd39d21711a077b6f2ae42fb45135"><strong>doc/SubreadUsersGuide.tex</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,19 +36,19 @@</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{center}</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="tex"><span class="p">{</span><span class="k" style="font-weight: 600;">\Huge\bf</span> Rsubread/Subread Users Guide<span class="p">}</span><span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="tex"><span class="k" style="font-weight: 600;">\vspace</span><span class="p">{</span>1 cm<span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" 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">

39

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<td class="diff-line-num new_line old" data-linenumber="39" 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="LC39" class="line" lang="tex"><span class="p">{</span><span class="k" style="font-weight: 600;">\centering\large</span> <span class="idiff left right">Rsubread v2.0.0/Subread v2.0</span>.0<span class="k" style="font-weight: 600;">\\</span><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(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="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

39

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

<pre style="margin: 0;">+<span id="LC39" class="line" lang="tex"><span class="p">{</span><span class="k" style="font-weight: 600;">\centering\large</span> <span class="idiff left right">Subread v2.0.1/Rsubread v2.2</span>.0<span class="k" style="font-weight: 600;">\\</span><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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

<pre style="margin: 0;"> <span id="LC40" class="line" lang="tex"><span class="k" style="font-weight: 600;">\vspace</span><span class="p">{</span>1 cm<span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="41" 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">

41

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<td class="diff-line-num new_line old" data-linenumber="41" 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>

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

<pre style="margin: 0;">-<span id="LC41" class="line" lang="tex"><span class="k" style="font-weight: 600;">\centering</span> <span class="idiff left right">2 September 2019</span><span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(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="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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

<pre style="margin: 0;">+<span id="LC41" class="line" lang="tex"><span class="k" style="font-weight: 600;">\centering</span> <span class="idiff left right">13 May 2020</span><span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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

<pre style="margin: 0;"> <span id="LC42" class="line" lang="tex"><span class="k" style="font-weight: 600;">\vspace</span><span class="p">{</span>5 cm<span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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

<pre style="margin: 0;"> <span id="LC43" class="line" lang="tex"><span class="k" style="font-weight: 600;">\Large</span> Wei Shi and Yang Liao<span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

</td>

<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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

<pre style="margin: 0;"> <span id="LC44" class="line" lang="tex"><span class="k" style="font-weight: 600;">\vspace</span><span class="p">{</span>1 cm<span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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

<pre style="margin: 0;"> <span id="LC45" class="line" lang="tex"><span class="k" style="font-weight: 600;">\small</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="46" 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">

46

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<td class="diff-line-num new_line old" data-linenumber="46" 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>

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

<pre style="margin: 0;">-<span id="LC46" class="line" lang="tex"><span class="p">{</span><span class="k" style="font-weight: 600;">\large</span> <span class="idiff left right">Bioinformatics Division</span><span class="k" style="font-weight: 600;">\\</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="47" 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">

47

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<td class="diff-line-num new_line old" data-linenumber="46" 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>

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

<pre style="margin: 0;">-<span id="LC47" class="line" lang="tex"><span class="idiff left right">The </span>Walter and Eliza Hall Institute of Medical Research<span class="k" style="font-weight: 600;">\\</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="48" 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">

48

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<td class="diff-line-num new_line old" data-linenumber="46" 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>

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

<pre style="margin: 0;">-<span id="LC48" class="line" lang="tex"><span class="idiff left right">The </span>University of Melbourne<span class="k" style="font-weight: 600;">\\</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="49" 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">

49

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<td class="diff-line-num new_line old" data-linenumber="46" 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>

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

<pre style="margin: 0;">-<span id="LC49" class="line" lang="tex"><span class="idiff left right">Melbourne, </span>Australia<span class="k" style="font-weight: 600;">\\</span><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(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="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

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

<pre style="margin: 0;">+<span id="LC46" class="line" lang="tex"><span class="p">{</span><span class="k" style="font-weight: 600;">\large</span> <span class="idiff left right">Olivia Newton-John Cancer Research Institute</span><span class="k" style="font-weight: 600;">\\</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(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="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

</td>

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

<pre style="margin: 0;">+<span id="LC47" class="line" lang="tex">Walter and Eliza Hall Institute of Medical Research<span class="k" style="font-weight: 600;">\\</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(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="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

48

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

<pre style="margin: 0;">+<span id="LC48" class="line" lang="tex">University of Melbourne<span class="k" style="font-weight: 600;">\\</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(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="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

49

</td>

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

<pre style="margin: 0;">+<span id="LC49" class="line" lang="tex">Australia<span class="k" style="font-weight: 600;">\\</span><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

</td>

<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

</td>

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

<pre style="margin: 0;"> <span id="LC50" class="line" lang="tex"><span class="k" style="font-weight: 600;">\vspace</span><span class="p">{</span>7 cm<span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="51" 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">

51

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<td class="diff-line-num new_line old" data-linenumber="51" 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>

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

<pre style="margin: 0;">-<span id="LC51" class="line" lang="tex"><span class="k" style="font-weight: 600;">\centering</span> Copyright <span class="k" style="font-weight: 600;">\small</span><span class="p">{</span><span class="k" style="font-weight: 600;">\copyright</span><span class="p">}</span>  2011 - 20<span class="idiff left right">19</span><span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="tex"><span class="k" style="font-weight: 600;">\centering</span> Copyright <span class="k" style="font-weight: 600;">\small</span><span class="p">{</span><span class="k" style="font-weight: 600;">\copyright</span><span class="p">}</span>  2011 - 20<span class="idiff left right">20</span><span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

52

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

52

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{center}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

53

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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

53

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{titlepage}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1027" style="width: 35px; color: rgba(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="1027" style="width: 35px; color: rgba(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">@@ -1027,7 +1027,7 @@ read mapping that produced the provided SAM/BAM files. This optional argument ca</td>

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<td class="diff-line-num old_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1027

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<td class="diff-line-num new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1027

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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="tex"><span class="k" style="font-weight: 600;">\hline</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1028

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<td class="diff-line-num new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1028

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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="tex">-s <span class="p">$</span><span class="nb" style="color: #0086b3;"><int or string></span><span class="p">$</span> <span class="k" style="font-weight: 600;">\newline</span> (<span class="k" style="font-weight: 600;">\code</span><span class="p">{</span>isStrandSpecific<span class="p">}</span>) <span class="p">&</span> Indicate if strand-specific read counting should be performed. A single integer value (applied to all input files) or a string of comma-separated values (applied to each corresponding input file) should be provided. Possible values include: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). Default value is 0 (ie. unstranded read counting carried out for all input files). For paired-end reads, strand of the first read is taken as the strand of the whole fragment. FLAG field is used to tell if a read is first or second read in a pair. Value of <span class="k" style="font-weight: 600;">\code</span><span class="p">{</span>isStrandSpecific<span class="p">}</span> parameter in <span class="p">{</span><span class="k" style="font-weight: 600;">\Rsubread</span><span class="p">}</span> <span class="p">{</span><span class="k" style="font-weight: 600;">\featureCounts</span><span class="p">}</span> is a vector which has a length of either <span class="p">{</span><span class="k" style="font-weight: 600;">\code</span><span class="p">{</span>1<span class="p">}}</span>, or the same with the total number of input files provided. <span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1029

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<td class="diff-line-num new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1029

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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="tex"><span class="k" style="font-weight: 600;">\hline</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1030" 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">

1030

</td>

<td class="diff-line-num new_line old" data-linenumber="1030" 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="LC1030" class="line" lang="tex">-t <span class="p">$</span><span class="nb" style="color: #0086b3;"><string></span><span class="p">$</span> <span class="k" style="font-weight: 600;">\newline</span> (<span class="k" style="font-weight: 600;">\code</span><span class="p">{</span>GTF.featureType<span class="p">}</span>) <span class="p">&</span> Specify the feature type<span class="idiff left right">. Only rows which have the</span> matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default.<span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1031" style="width: 35px; color: rgba(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="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1030

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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="tex">-t <span class="p">$</span><span class="nb" style="color: #0086b3;"><string></span><span class="p">$</span> <span class="k" style="font-weight: 600;">\newline</span> (<span class="k" style="font-weight: 600;">\code</span><span class="p">{</span>GTF.featureType<span class="p">}</span>) <span class="p">&</span> Specify the feature type<span class="idiff left right">(s). If more than one feature type is provided, they should be separated by `,' (no space). Only rows which have a</span> matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default.<span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1031

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<td class="diff-line-num new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1031

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

<pre style="margin: 0;"> <span id="LC1031" class="line" lang="tex"><span class="k" style="font-weight: 600;">\hline</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1032

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<td class="diff-line-num new_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1032

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<pre style="margin: 0;"> <span id="LC1032" class="line" lang="tex">-T <span class="p">$</span><span class="nb" style="color: #0086b3;"><int></span><span class="p">$</span> <span class="k" style="font-weight: 600;">\newline</span> (<span class="k" style="font-weight: 600;">\code</span><span class="p">{</span>nthreads<span class="p">}</span>) <span class="p">&</span> Number of the threads. The value should be between 1 and 32. 1 by default.<span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1033

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<td class="diff-line-num new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1033

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<pre style="margin: 0;"> <span id="LC1033" class="line" lang="tex"><span class="k" style="font-weight: 600;">\hline</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1190" style="width: 35px; color: rgba(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="1190" style="width: 35px; color: rgba(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">@@ -1190,6 +1190,17 @@ featureCounts(files="mapping_results_PE.bam",isPairedEnd=TRUE,requireBothEndsMap</td>

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<td class="diff-line-num old_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1190

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<td class="diff-line-num new_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1190

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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="tex">featureCounts(files="mapping<span class="p">_</span>results<span class="p">_</span>PE.bam",isPairedEnd=TRUE,countChimericFragments=FALSE)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1191

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<td class="diff-line-num new_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1191

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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{Rcode}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1192

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<td class="diff-line-num new_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1192

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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(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="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="tex"><span class="k" style="font-weight: 600;">\chapter</span><span class="p">{</span>Mapping and quantification of single-cell data<span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(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="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>cellCounts<span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(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="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1196

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

<pre style="margin: 0;">+<span id="LC1196" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(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="1197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1197

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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="tex">The <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>cellCounts<span class="p">}</span> program was developed to process single-cell RNA-seq (scRNA-seq) data to generate UMI counts for genes, exons or other genomic features.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(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="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1198

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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="tex">It calls <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>align<span class="p">}</span> function to perform mapping of scRNA-seq reads and calls <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>featureCounts<span class="p">}</span> functions to generate UMI counts.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(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="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="tex"><span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>cellCounts<span class="p">}</span> demultiplexes cell barcodes and also deduplicates reads.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(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="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1200

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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="tex">It accepts BCL or FASTQ files as input.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(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="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="tex">Quantification of a scRNA-seq dataset can be simply done by a single <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>cellCounts<span class="p">}</span> function call.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(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="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1202

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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="tex">It is much faster than other scRNA-seq quantification tools.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(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="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1203

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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1204" style="width: 35px; color: rgba(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="LC1204" class="line" lang="tex"><span class="k" style="font-weight: 600;">\chapter</span><span class="p">{</span>SNP calling<span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1194

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<td class="diff-line-num new_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1205

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<pre style="margin: 0;"> <span id="LC1205" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1195

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<td class="diff-line-num new_line" data-linenumber="1206" style="width: 35px; color: rgba(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="LC1206" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Algorithm<span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="7079f81404dcaadc0154c53a419b2d1cb5f253e6">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#7079f81404dcaadc0154c53a419b2d1cb5f253e6"><strong>src/HelperFunctions.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1235" style="width: 35px; color: rgba(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="1235" style="width: 35px; color: rgba(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">@@ -1235,10 +1235,12 @@ HashTable * load_alias_table(char * fname) {</td>

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<pre style="margin: 0;"> <span id="LC1235" 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;">sam_chr</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;">anno_chr</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1236

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<td class="diff-line-num new_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1236

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<pre style="margin: 0;"> <span id="LC1236" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1237" style="width: 35px; color: rgba(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="LC1237" class="line" lang="c">           <span class="n" style="color: #333;">sam_chr</span><span class="p">[</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">sam_chr</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1238" style="width: 35px; color: rgba(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="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">sam_chr</span><span class="p">[</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">sam_chr</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'\r'</span><span class="p">)</span> <span class="n" style="color: #333;">sam_chr</span><span class="p">[</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">sam_chr</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1239" style="width: 35px; color: rgba(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="LC1239" 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;">anno_chr_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">anno_chr</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1240" style="width: 35px; color: rgba(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="LC1240" class="line" lang="c">           <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">anno_chr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">anno_chr</span><span class="p">);</span></span>

</pre>

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1240

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<td class="diff-line-num new_line" data-linenumber="1241" style="width: 35px; color: rgba(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="LC1241" 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;">sam_chr_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">sam_chr</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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1241

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<td class="diff-line-num new_line" data-linenumber="1242" style="width: 35px; color: rgba(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="LC1242" class="line" lang="c">           <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">sam_chr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">sam_chr</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1242" style="width: 35px; color: rgba(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="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//             SUBREADprintf("ALIAS_LOAD : '%s' => '%s'\n", sam_chr_buf, anno_chr_buf);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1244

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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="c">           <span class="n" style="color: #333;">HashTablePut</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">sam_chr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">anno_chr_buf</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1245" style="width: 35px; color: rgba(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="LC1245" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1246

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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="c"></span>

</pre>

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<br>

</li>

<li id="ecc92c74c51f8b1692fd1bd13b9657e456522c0a">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#ecc92c74c51f8b1692fd1bd13b9657e456522c0a"><strong>src/core-interface-aligner.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" style="width: 35px; color: rgba(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="68" style="width: 35px; color: rgba(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">@@ -68,6 +68,7 @@ static struct option long_options[] =</td>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c">     <span class="p">{</span><span class="s" style="color: #d14;">"multiMapping"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="69" style="width: 35px; color: rgba(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="LC69" class="line" lang="c">     <span class="p">{</span><span class="s" style="color: #d14;">"keepReadOrder"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(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="LC70" class="line" lang="c">     <span class="p">{</span><span class="s" style="color: #d14;">"sortReadsByCoordinates"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="71" style="width: 35px; color: rgba(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="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c">     <span class="p">{</span><span class="s" style="color: #d14;">"noTLENpreference"</span><span class="p">,</span>  <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

72

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c">     <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

72

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<td class="diff-line-num new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

74

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

<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="583" style="width: 35px; color: rgba(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="584" style="width: 35px; color: rgba(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">@@ -583,6 +584,10 @@ int parse_opts_aligner(int argc , char ** argv, global_context_t * global_contex</td>

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<pre style="margin: 0;"> <span id="LC584" class="line" lang="c">                                    <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">use_memory_buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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584

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<td class="diff-line-num new_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">

585

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<pre style="margin: 0;"> <span id="LC585" class="line" lang="c">                                    <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">reads_per_chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">600llu</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>

</pre>

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585

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<td class="diff-line-num new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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<td class="diff-line-num new new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC587" class="line" lang="c">                            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="s" style="color: #d14;">"noTLENpreference"</span><span class="p">,</span> <span class="n" style="color: #333;">long_options</span><span class="p">[</span><span class="n" style="color: #333;">option_index</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC588" class="line" lang="c">                            <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC589" class="line" lang="c">                                    <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">no_TLEN_preference</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC590" class="line" lang="c">                            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC591" class="line" lang="c">                            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="s" style="color: #d14;">"gtfFeature"</span><span class="p">,</span> <span class="n" style="color: #333;">long_options</span><span class="p">[</span><span class="n" style="color: #333;">option_index</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC592" class="line" lang="c">                            <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC593" class="line" lang="c">                                    <span class="n" style="color: #333;">strncpy</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">exon_annotation_feature_name_column</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_READ_NAME_LEN</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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<br>

</li>

<li id="d7c9610d0bb39f36045810aea42dfc930a2d041f">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#d7c9610d0bb39f36045810aea42dfc930a2d041f"><strong>src/core-junction.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1106" style="width: 35px; color: rgba(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="1106" style="width: 35px; color: rgba(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">@@ -1106,7 +1106,7 @@ void copy_vote_to_alignment_res(global_context_t * global_context, thread_contex</td>

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<pre style="margin: 0;"> <span id="LC1106" class="line" lang="c">                                   <span class="c1" style="color: #998; font-style: italic;">// if the covered region has a wrong arrangement to their relative positions.</span></span>

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<pre style="margin: 0;"> <span id="LC1107" class="line" lang="c">                                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">test_minor_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">test_junction_minor</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span><span class="p">,</span> <span class="n" style="color: #333;">current_vote</span><span class="p">,</span> <span class="n" style="color: #333;">vote_i</span><span class="p">,</span> <span class="n" style="color: #333;">vote_j</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">dist</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//#warning " ============ DEBUG 1 ==================== "</span></span>

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<td class="diff-line-num new_line old" data-linenumber="1109" 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="LC1109" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left right"> </span><span class="n" style="color: #333;">FIXLENstrcmp</span><span class="p">(</span><span class="s" style="color: #d14;">"R002403247"</span><span class="p">,</span> <span class="n" style="color: #333;">read_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">FIXLENstrcmp</span><span class="p">(</span><span class="s" style="color: #d14;">"R002403247"</span><span class="p">,</span> <span class="n" style="color: #333;">read_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="c">                                           <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">posout2</span><span class="p">[</span><span class="mi" style="color: #099;">100</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1111

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<td class="diff-line-num new_line" data-linenumber="1111" style="width: 35px; color: rgba(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="LC1111" class="line" lang="c">                                           <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">posout1</span><span class="p">[</span><span class="mi" style="color: #099;">100</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1112" style="width: 35px; color: rgba(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="LC1112" class="line" lang="c">                                           <span class="n" style="color: #333;">absoffset_to_posstr</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">current_vote</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">pos</span><span class="p">[</span><span class="n" style="color: #333;">vote_i</span><span class="p">][</span><span class="n" style="color: #333;">vote_j</span><span class="p">],</span> <span class="n" style="color: #333;">posout1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2402" style="width: 35px; color: rgba(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="2402" style="width: 35px; color: rgba(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">@@ -2402,7 +2402,6 @@ int process_voting_junction_PE_topK(global_context_t * global_context, thread_co</td>

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<td class="diff-line-num old_line" data-linenumber="2402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2402" style="width: 35px; color: rgba(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="LC2402" class="line" lang="c">                           <span class="n" style="color: #333;">simple_mapping_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">current_loc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_second_read</span><span class="o" style="font-weight: 600;">?</span><span class="n" style="color: #333;">comb_buffer</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">r2_loc</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">comb_buffer</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">r1_loc</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2403" style="width: 35px; color: rgba(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="LC2403" class="line" lang="c">                           <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">current_loc</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2404" style="width: 35px; color: rgba(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="LC2404" class="line" lang="c">                           <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_loc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mapping_position</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="2405" 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="LC2405" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("CLLL BUF %d R_%d : %u\n", i, 1+is_second_read,  current_loc->mapping_position);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2405

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<pre style="margin: 0;"> <span id="LC2405" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2407

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<td class="diff-line-num new_line" data-linenumber="2406" style="width: 35px; color: rgba(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="LC2406" class="line" lang="c">                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">is_exist</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2407" style="width: 35px; color: rgba(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="LC2407" class="line" lang="c">                           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">current_r_cursor</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2412" style="width: 35px; color: rgba(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="2411" style="width: 35px; color: rgba(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">@@ -2412,6 +2411,7 @@ int process_voting_junction_PE_topK(global_context_t * global_context, thread_co</td>

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<td class="diff-line-num old_line" data-linenumber="2412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2412

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<td class="diff-line-num new_line" data-linenumber="2411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2411

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<pre style="margin: 0;"> <span id="LC2411" class="line" lang="c">                                           <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2413

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<td class="diff-line-num new_line" data-linenumber="2412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2412

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<pre style="margin: 0;"> <span id="LC2412" class="line" lang="c">                                   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2414

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<td class="diff-line-num new_line" data-linenumber="2413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2413

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<pre style="margin: 0;"> <span id="LC2413" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2415" style="width: 35px; color: rgba(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="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2414

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<pre style="margin: 0;">+<span id="LC2414" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("CLLL BUF %d R_%d : %u ; EXIST %d. Written into the %d-th best location\n", i, 1+is_second_read,  current_loc->mapping_position, is_exist, *current_r_cursor);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2415

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

<pre style="margin: 0;"> <span id="LC2415" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2416

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<pre style="margin: 0;"> <span id="LC2416" 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;">is_exist</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2417" style="width: 35px; color: rgba(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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2417

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<pre style="margin: 0;"> <span id="LC2417" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">current_loc</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_vote_t_item</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2984" style="width: 35px; color: rgba(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="2984" style="width: 35px; color: rgba(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">@@ -2984,9 +2984,10 @@ int final_CIGAR_quality(global_context_t * global_context, thread_context_t * th</td>

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<td class="diff-line-num old_line" data-linenumber="2984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2984

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<td class="diff-line-num new_line" data-linenumber="2984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2984

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<pre style="margin: 0;"> <span id="LC2984" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2985

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<td class="diff-line-num new_line" data-linenumber="2985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2985

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<pre style="margin: 0;"> <span id="LC2985" class="line" lang="c">                                           <span class="n" style="color: #333;">tail_soft_clipped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_soft_clipping</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span><span class="p">,</span> <span class="n" style="color: #333;">current_value_index</span><span class="p">,</span> <span class="n" style="color: #333;">read_text</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read_cursor</span><span class="p">,</span> <span class="n" style="color: #333;">current_perfect_section_abs</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_int</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">adj_coverage_end</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2986

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<td class="diff-line-num new_line" data-linenumber="2986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2986

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<pre style="margin: 0;"> <span id="LC2986" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2987" 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">

2987

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<td class="diff-line-num new_line old" data-linenumber="2987" 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="LC2987" class="line" lang="c">                                   <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("SSTAIL:%d\n", tail_soft_clipped);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2988" style="width: 35px; color: rgba(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="2987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2987

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<pre style="margin: 0;">+<span id="LC2987" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">FIXLENstrcmp</span><span class="p">(</span><span class="s" style="color: #d14;">"NS500643:556:HGTMTBGXB:4:13403:18179:8012"</span><span class="p">,</span> <span class="n" style="color: #333;">read_name</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2988" style="width: 35px; color: rgba(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="2988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2988

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<pre style="margin: 0;">+<span id="LC2988" class="line" lang="c">                                           <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"SSTAIL:%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">tail_soft_clipped</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2988

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<td class="diff-line-num new_line" data-linenumber="2989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2989

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<pre style="margin: 0;"> <span id="LC2989" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2989" 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">

2989

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<td class="diff-line-num new_line old" data-linenumber="2990" 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="LC2989" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tail_soft_clipped</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">tmp_int</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2990" style="width: 35px; color: rgba(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="2990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2990

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<pre style="margin: 0;">+<span id="LC2990" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">tail_soft_clipped</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">tmp_int</span><span class="p">){</span></span>

</pre>

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2990

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<td class="diff-line-num new_line" data-linenumber="2991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2991

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<pre style="margin: 0;"> <span id="LC2991" class="line" lang="c">                                           <span class="n" style="color: #333;">tail_soft_clipped</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2991

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<td class="diff-line-num new_line" data-linenumber="2992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2992

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<pre style="margin: 0;"> <span id="LC2992" class="line" lang="c">                                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">full_section_clipped</span><span class="p">)(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">full_section_clipped</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2992

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<td class="diff-line-num new_line" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2993

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<pre style="margin: 0;"> <span id="LC2993" class="line" lang="c">                                   <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">has_clipping_this_section_tail</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3125" style="width: 35px; color: rgba(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="3126" style="width: 35px; color: rgba(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">@@ -3125,6 +3126,8 @@ int final_CIGAR_quality(global_context_t * global_context, thread_context_t * th</td>

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<td class="diff-line-num old_line" data-linenumber="3125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3125

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<td class="diff-line-num new_line" data-linenumber="3126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3126

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<pre style="margin: 0;"> <span id="LC3126" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3126

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<td class="diff-line-num new_line" data-linenumber="3127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3127

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<pre style="margin: 0;"> <span id="LC3127" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3127

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<td class="diff-line-num new_line" data-linenumber="3128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3128

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<pre style="margin: 0;"> <span id="LC3128" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3128" style="width: 35px; color: rgba(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="3129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3129" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">FIXLENstrcmp</span><span class="p">(</span><span class="s" style="color: #d14;">"NS500643:556:HGTMTBGXB:4:13403:18179:8012"</span><span class="p">,</span> <span class="n" style="color: #333;">read_name</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3128" style="width: 35px; color: rgba(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="3130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3130" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"NEW_CIGAR_2 : %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">new_cigar_tmp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3128

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<td class="diff-line-num new_line" data-linenumber="3131" style="width: 35px; color: rgba(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="LC3131" class="line" lang="c">           <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">cigar_string</span><span class="p">,</span> <span class="n" style="color: #333;">new_cigar_tmp</span><span class="p">);</span></span>

</pre>

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3129

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<td class="diff-line-num new_line" data-linenumber="3132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3132

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<pre style="margin: 0;"> <span id="LC3132" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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3130

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<td class="diff-line-num new_line" data-linenumber="3133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3133

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<pre style="margin: 0;"> <span id="LC3133" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3347" style="width: 35px; color: rgba(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="3350" style="width: 35px; color: rgba(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">@@ -3347,11 +3350,11 @@ unsigned int finalise_explain_CIGAR(global_context_t * global_context, thread_co</td>

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3347

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<pre style="margin: 0;"> <span id="LC3350" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3351" style="width: 35px; color: rgba(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="LC3351" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3349

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<td class="diff-line-num new_line" data-linenumber="3352" style="width: 35px; color: rgba(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="LC3352" class="line" lang="c">                   <span class="c1" style="color: #998; font-style: italic;">//#warning " ========== COMMENT THIS LINE !! ========="</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3350" 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">

3350

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<td class="diff-line-num new_line old" data-linenumber="3353" 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="LC3350" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">FIXLENstrcmp</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"R00000110641</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">explain_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">read_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3351" style="width: 35px; color: rgba(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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3353

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<pre style="margin: 0;">+<span id="LC3353" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">1</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">FIXLENstrcmp</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"NS500643:556:HGTMTBGXB:4:13403:18179:8012</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">explain_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">read_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

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3351

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<td class="diff-line-num new_line" data-linenumber="3354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3354

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<pre style="margin: 0;"> <span id="LC3354" class="line" lang="c">                           <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">outpos1</span><span class="p">[</span><span class="mi" style="color: #099;">100</span><span class="p">];</span></span>

</pre>

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3352

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<td class="diff-line-num new_line" data-linenumber="3355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3355

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<pre style="margin: 0;"> <span id="LC3355" class="line" lang="c">                           <span class="n" style="color: #333;">absoffset_to_posstr</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">final_position</span><span class="p">,</span> <span class="n" style="color: #333;">outpos1</span><span class="p">);</span></span>

</pre>

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3353

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<td class="diff-line-num new_line" data-linenumber="3356" style="width: 35px; color: rgba(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="LC3356" class="line" lang="c">                           <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"FINALQUAL %s : FINAL_POS=%s ( %u )</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">CIGAR=%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">MM=%d / MAPLEN=%d > %d?</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VOTE=%d > %0.2f x %d ?  MASK=%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">QUAL=%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">BRNO=%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">KNOWN_JUNCS=%d PENALTY=%d</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">explain_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">read_name</span><span class="p">,</span> <span class="n" style="color: #333;">outpos1</span> <span class="p">,</span> <span class="n" style="color: #333;">final_position</span> <span class="p">,</span> <span class="n" style="color: #333;">tmp_cigar</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch_bases</span><span class="p">,</span> <span class="n" style="color: #333;">non_clipped_length</span><span class="p">,</span> <span class="n" style="color: #333;">applied_mismatch</span><span class="p">,</span>  <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">selected_votes</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">minimum_exonic_subread_fraction</span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">used_subreads_in_vote</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">result_flags</span><span class="p">,</span> <span class="n" style="color: #333;">final_qual</span><span class="p">,</span> <span class="n" style="color: #333;">explain_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">best_read_id</span><span class="p">,</span> <span class="n" style="color: #333;">known_junction_supp</span><span class="p">,</span> <span class="n" style="color: #333;">explain_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">best_indel_penalty</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="3357" 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="LC3354" class="line" lang="c">                           <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3355" style="width: 35px; color: rgba(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="3357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3357

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<pre style="margin: 0;">+<span id="LC3357" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>exit(0);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3355

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<td class="diff-line-num new_line" data-linenumber="3358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3358

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<pre style="margin: 0;"> <span id="LC3358" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3356

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<td class="diff-line-num new_line" data-linenumber="3359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3359

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<pre style="margin: 0;"> <span id="LC3359" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3357

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<td class="diff-line-num new_line" data-linenumber="3360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3360

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

<pre style="margin: 0;"> <span id="LC3360" class="line" lang="c"></span>

</pre>

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<br>

</li>

<li id="a26ea438a2b6aee04f419d17c87da7e9b997e7ae">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#a26ea438a2b6aee04f419d17c87da7e9b997e7ae"><strong>src/core.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2676" style="width: 35px; color: rgba(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="2676" style="width: 35px; color: rgba(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">@@ -2676,7 +2676,7 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa</td>

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2676

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<td class="diff-line-num new_line" data-linenumber="2676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2676

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<pre style="margin: 0;"> <span id="LC2676" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">current_result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">selected_votes</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">minimum_subread_for_second_read</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">max_votes</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">minimum_subread_for_first_read</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2677

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<td class="diff-line-num new_line" data-linenumber="2677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2677

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<pre style="margin: 0;"> <span id="LC2677" class="line" lang="c">                           <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2678

</td>

<td class="diff-line-num new_line" data-linenumber="2678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2678

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<pre style="margin: 0;"> <span id="LC2678" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//  if(current_read_number == 111 || current_read_number == 112)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2679" 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">

2679

</td>

<td class="diff-line-num new_line old" data-linenumber="2679" 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="LC2679" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//   SUBREADprintf("RESET0 [%</span>d] R_%d SEL=%d MAX=%d\n", current_read_number, is_second_read + 1, current_result->selected_votes, max_votes);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2680" style="width: 35px; color: rgba(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="2679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2679

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<pre style="margin: 0;">+<span id="LC2679" class="line" lang="c">                           <span class="idiff left">       </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//SUBREADprintf("RESET0 [%ll</span>d] R_%d SEL=%d MAX=%d\n", current_read_number, is_second_read + 1, current_result->selected_votes, max_votes);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2680

</td>

<td class="diff-line-num new_line" data-linenumber="2680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2680

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<pre style="margin: 0;"> <span id="LC2680" class="line" lang="c">                                   <span class="n" style="color: #333;">current_result</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">selected_votes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2681

</td>

<td class="diff-line-num new_line" data-linenumber="2681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2681

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<pre style="margin: 0;"> <span id="LC2681" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2682

</td>

<td class="diff-line-num new_line" data-linenumber="2682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2682

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

<pre style="margin: 0;"> <span id="LC2682" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

</td>

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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="2688" style="width: 35px; color: rgba(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="2688" style="width: 35px; color: rgba(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">@@ -2688,7 +2688,7 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa</td>

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<td class="diff-line-num old_line" data-linenumber="2688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2688

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<td class="diff-line-num new_line" data-linenumber="2688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2688

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<pre style="margin: 0;"> <span id="LC2688" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2689

</td>

<td class="diff-line-num new_line" data-linenumber="2689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2689

</td>

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

<pre style="margin: 0;"> <span id="LC2689" class="line" lang="c"></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="2690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2690

</td>

<td class="diff-line-num new_line" data-linenumber="2690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2690

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<pre style="margin: 0;"> <span id="LC2690" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//#warning ">>>>>>> COMMENT THIS <<<<<<<"</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2691" 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">

2691

</td>

<td class="diff-line-num new_line old" data-linenumber="2691" 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="LC2691" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//printf("OCT27-STEP21-%s:%d-ALN%02d-THRE %d<span class="idiff left right">\n", current_read_name, is_second_read + 1, best_read_id, thread_context -> thread_id</span>);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2692" style="width: 35px; color: rgba(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="2691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2691" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//printf("OCT27-STEP21-%s:%d-ALN%02d-THRE %d<span class="idiff left right"> in MM=%d\n", current_read_name, is_second_read + 1, best_read_id, thread_context -> thread_id, global_context -> config.multi_best_reads</span>);</span></span>

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<pre style="margin: 0;"> <span id="LC2692" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2693" class="line" lang="c">                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">is_negative_strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">current_result</span>  <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">result_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CORE_IS_NEGATIVE_STRAND</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2694" style="width: 35px; color: rgba(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="LC2694" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2844" style="width: 35px; color: rgba(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="2844" style="width: 35px; color: rgba(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">@@ -2844,7 +2844,7 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa</td>

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<td class="diff-line-num new_line" data-linenumber="2844" style="width: 35px; color: rgba(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="LC2844" class="line" lang="c">                                   <span class="n" style="color: #333;">test_PE_and_same_chro_align</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="p">,</span> <span class="n" style="color: #333;">realignment_result_R1</span> <span class="p">,</span> <span class="n" style="color: #333;">realignment_result_R2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">is_exonic_regions</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">is_PE</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">is_same_chro</span> <span class="p">,</span> <span class="n" style="color: #333;">read_len_1</span><span class="p">,</span> <span class="n" style="color: #333;">read_len_2</span><span class="p">,</span> <span class="n" style="color: #333;">read_name_1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tlen</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="2845" style="width: 35px; color: rgba(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="LC2845" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2846" style="width: 35px; color: rgba(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="LC2846" class="line" lang="c">                                   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">TLEN_exp_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="2847" 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="LC2847" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">is_PE</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">reported_multi_best_reads</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2847" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">is_PE</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">no_TLEN_preference</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">global_context</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">config</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">reported_multi_best_reads</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2848" style="width: 35px; color: rgba(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="LC2848" class="line" lang="c">                                           <span class="n" style="color: #333;">TLEN_exp_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">tlen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">expected_TLEN</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span><span class="p">(</span><span class="n" style="color: #333;">tlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">expected_TLEN</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span><span class="p">(</span><span class="n" style="color: #333;">expected_TLEN</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tlen</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="2849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2849" style="width: 35px; color: rgba(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="LC2849" class="line" lang="c">                                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">TLEN_exp_score</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">999</span><span class="p">)</span> <span class="n" style="color: #333;">TLEN_exp_score</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2850" style="width: 35px; color: rgba(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="LC2850" class="line" lang="c">                                           <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">TLEN_exp_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">999</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">TLEN_exp_score</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3017" style="width: 35px; color: rgba(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="3017" style="width: 35px; color: rgba(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">@@ -3017,6 +3017,7 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa</td>

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<pre style="margin: 0;"> <span id="LC3017" class="line" lang="c">   <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC3018" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3019

</td>

<td class="diff-line-num new_line" data-linenumber="3019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3019

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<pre style="margin: 0;"> <span id="LC3019" class="line" lang="c">   <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">final_realignments</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3020" style="width: 35px; color: rgba(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="3020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3020

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<pre style="margin: 0;">+<span id="LC3020" class="line" lang="c">   <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">final_realignment_number</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3020

</td>

<td class="diff-line-num new_line" data-linenumber="3021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3021

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<pre style="margin: 0;"> <span id="LC3021" class="line" lang="c">   <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">final_MATCH_buffer1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3021

</td>

<td class="diff-line-num new_line" data-linenumber="3022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3022

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<pre style="margin: 0;"> <span id="LC3022" class="line" lang="c">   <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">final_MISMATCH_buffer1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3022

</td>

<td class="diff-line-num new_line" data-linenumber="3023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3023

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<pre style="margin: 0;"> <span id="LC3023" class="line" lang="c">   <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">final_PENALTY_buffer1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3248" style="width: 35px; color: rgba(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="3249" style="width: 35px; color: rgba(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">@@ -3248,7 +3249,7 @@ int do_voting(global_context_t * global_context, thread_context_t * thread_conte</td>

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<td class="diff-line-num old_line" data-linenumber="3248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3248

</td>

<td class="diff-line-num new_line" data-linenumber="3249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3249

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<pre style="margin: 0;"> <span id="LC3249" class="line" lang="c">                                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">" ======= PAIR %s = %llu ; NON_INFORMATIVE = %d, %d =======</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">read_name_1</span><span class="p">,</span> <span class="n" style="color: #333;">current_read_number</span><span class="p">,</span> <span class="n" style="color: #333;">vote_1</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">noninformative_subreads</span><span class="p">,</span> <span class="n" style="color: #333;">vote_2</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">noninformative_subreads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3249

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<td class="diff-line-num new_line" data-linenumber="3250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3250

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<pre style="margin: 0;"> <span id="LC3250" class="line" lang="c">                                   <span class="n" style="color: #333;">print_votes</span><span class="p">(</span><span class="n" style="color: #333;">vote_1</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">index_prefix</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3250

</td>

<td class="diff-line-num new_line" data-linenumber="3251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3251

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<pre style="margin: 0;"> <span id="LC3251" class="line" lang="c">                                   <span class="n" style="color: #333;">print_votes</span><span class="p">(</span><span class="n" style="color: #333;">vote_2</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">index_prefix</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3251" 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">

3251

</td>

<td class="diff-line-num new_line old" data-linenumber="3252" 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="LC3251" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">is_reversed</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;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3252" style="width: 35px; color: rgba(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="3252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3252

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<pre style="margin: 0;">+<span id="LC3252" class="line" lang="c">                                   <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>if(is_reversed==1)exit(0);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3252

</td>

<td class="diff-line-num new_line" data-linenumber="3253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3253

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<pre style="margin: 0;"> <span id="LC3253" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3253

</td>

<td class="diff-line-num new_line" data-linenumber="3254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3254

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

<pre style="margin: 0;"> <span id="LC3254" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3254

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<td class="diff-line-num new_line" data-linenumber="3255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3255

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<pre style="margin: 0;"> <span id="LC3255" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_reads</span><span class="p">.</span><span class="n" style="color: #333;">is_paired_end_reads</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3615" style="width: 35px; color: rgba(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="3616" style="width: 35px; color: rgba(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">@@ -3615,6 +3616,7 @@ int read_chunk_circles(global_context_t *global_context)</td>

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<td class="diff-line-num old_line" data-linenumber="3615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3615

</td>

<td class="diff-line-num new_line" data-linenumber="3616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3616

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<pre style="margin: 0;"> <span id="LC3616" class="line" lang="c">                           <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"Load the %d-th index block..."</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_index_block_number</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3616

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<td class="diff-line-num new_line" data-linenumber="3617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3617

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

<pre style="margin: 0;"> <span id="LC3617" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3617

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<td class="diff-line-num new_line" data-linenumber="3618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3618

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<pre style="margin: 0;"> <span id="LC3618" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gehash_load</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_index</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_fname</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3618" style="width: 35px; color: rgba(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="3619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3619

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<pre style="margin: 0;">+<span id="LC3619" class="line" lang="c">                           <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"The index block has been loaded."</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3618

</td>

<td class="diff-line-num new_line" data-linenumber="3620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3620

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<pre style="margin: 0;"> <span id="LC3620" class="line" lang="c">                           <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tmp_fname</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.%02d.%c.array"</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">index_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_index_block_number</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">space_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">GENE_SPACE_COLOR</span><span class="o" style="font-weight: 600;">?</span><span class="sc" style="color: #d14;">'c'</span><span class="o" style="font-weight: 600;">:</span><span class="sc" style="color: #d14;">'b'</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3619

</td>

<td class="diff-line-num new_line" data-linenumber="3621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3621

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<pre style="margin: 0;"> <span id="LC3621" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3620

</td>

<td class="diff-line-num new_line" data-linenumber="3622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3622

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<pre style="margin: 0;"> <span id="LC3622" class="line" lang="c">                   <span class="n" style="color: #333;">period_load_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">miltime</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">time_load_index</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3628" style="width: 35px; color: rgba(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="3630" style="width: 35px; color: rgba(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">@@ -3628,6 +3630,7 @@ int read_chunk_circles(global_context_t *global_context)</td>

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<td class="diff-line-num old_line" data-linenumber="3628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3628

</td>

<td class="diff-line-num new_line" data-linenumber="3630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3630

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<pre style="margin: 0;"> <span id="LC3630" class="line" lang="c">                           <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_final_voting_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3629

</td>

<td class="diff-line-num new_line" data-linenumber="3631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3631

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<pre style="margin: 0;"> <span id="LC3631" class="line" lang="c">                   <span class="k" style="font-weight: 600;">else</span>   <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_final_voting_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3630

</td>

<td class="diff-line-num new_line" data-linenumber="3632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3632

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

<pre style="margin: 0;"> <span id="LC3632" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3631" style="width: 35px; color: rgba(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="3633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3633

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<pre style="margin: 0;">+<span id="LC3633" class="line" lang="c">                   <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"Start read mapping in chunk."</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3631

</td>

<td class="diff-line-num new_line" data-linenumber="3634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3634

</td>

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

<pre style="margin: 0;"> <span id="LC3634" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">time_start_voting</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">miltime</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3632

</td>

<td class="diff-line-num new_line" data-linenumber="3635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3635

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

<pre style="margin: 0;"> <span id="LC3635" class="line" lang="c">                   <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_maybe_threads</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">STEP_VOTING</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3633

</td>

<td class="diff-line-num new_line" data-linenumber="3636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3636

</td>

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

<pre style="margin: 0;"> <span id="LC3636" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">period_voting</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">miltime</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">time_start_voting</span><span class="p">;</span></span>

</pre>

</td>

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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="3980" style="width: 35px; color: rgba(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="3983" style="width: 35px; color: rgba(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">@@ -3980,12 +3983,46 @@ int do_anno_bitmap_add_feature(char * gene_name, char * tracnscript_id, char * c</td>

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<td class="diff-line-num old_line" data-linenumber="3980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3980

</td>

<td class="diff-line-num new_line" data-linenumber="3983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3983

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<pre style="margin: 0;"> <span id="LC3983" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3981

</td>

<td class="diff-line-num new_line" data-linenumber="3984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3984

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

<pre style="margin: 0;"> <span id="LC3984" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3982

</td>

<td class="diff-line-num new_line" data-linenumber="3985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3985

</td>

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

<pre style="margin: 0;"> <span id="LC3985" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="3983" 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">

3983

</td>

<td class="diff-line-num new_line old" data-linenumber="3986" 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>

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

<pre style="margin: 0;">-<span id="LC3983" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">warning_anno_vs_index</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">anno_chros_tab</span><span class="p">,</span> <span class="n" style="color: #333;">gene_offset_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">index_chros_offset</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="3984" 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">

3984

</td>

<td class="diff-line-num new_line old" data-linenumber="3986" 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>

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

<pre style="margin: 0;">-<span id="LC3984" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span>  <span class="n" style="color: #333;">index_chros_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index_chros_offset</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">read_name_to_index</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="3985" 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">

3985

</td>

<td class="diff-line-num new_line old" data-linenumber="3986" 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>

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

<pre style="margin: 0;">-<span id="LC3985" class="line" lang="c">   <span class="n" style="color: #333;">warning_hash_hash</span><span class="p">(</span><span class="n" style="color: #333;">anno_chros_tab</span><span class="p">,</span> <span class="n" style="color: #333;">index_chros_tab</span><span class="p">,</span> <span class="s" style="color: #d14;">"Chromosomes/contigs in annotation but not in index :"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="3986" 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">

3986

</td>

<td class="diff-line-num new_line old" data-linenumber="3986" 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>

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

<pre style="margin: 0;">-<span id="LC3986" class="line" lang="c">   <span class="n" style="color: #333;">warning_hash_hash</span><span class="p">(</span><span class="n" style="color: #333;">index_chros_tab</span><span class="p">,</span> <span class="n" style="color: #333;">anno_chros_tab</span><span class="p">,</span> <span class="s" style="color: #d14;">"Chromosomes/contigs in index but not in annotation :"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3987" style="width: 35px; color: rgba(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="3986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3986

</td>

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

<pre style="margin: 0;">+<span id="LC3986" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">convert_table_key_to_alias</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;">ky</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;">va</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tab</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3987" style="width: 35px; color: rgba(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="3987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3987

</td>

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

<pre style="margin: 0;">+<span id="LC3987" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alias_index_to_annot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix2</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3987" style="width: 35px; color: rgba(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="3988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3988

</td>

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

<pre style="margin: 0;">+<span id="LC3988" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result_annot_chros</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3987" style="width: 35px; color: rgba(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="3989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3989

</td>

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

<pre style="margin: 0;">+<span id="LC3989" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3987" style="width: 35px; color: rgba(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="3990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3990

</td>

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

<pre style="margin: 0;">+<span id="LC3990" 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;">index_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ky</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3987" style="width: 35px; color: rgba(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="3991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3991

</td>

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

<pre style="margin: 0;">+<span id="LC3991" 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;">annot_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">alias_index_to_annot</span><span class="p">,</span> <span class="n" style="color: #333;">index_name</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3987" style="width: 35px; color: rgba(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="3992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3992

</td>

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

<pre style="margin: 0;">+<span id="LC3992" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">annot_name</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">annot_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index_name</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3987" style="width: 35px; color: rgba(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="3993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3993

</td>

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

<pre style="margin: 0;">+<span id="LC3993" class="line" lang="c">   <span class="n" style="color: #333;">HashTablePut</span><span class="p">(</span> <span class="n" style="color: #333;">result_annot_chros</span><span class="p">,</span> <span class="n" style="color: #333;">annot_name</span><span class="p">,</span> <span class="n" style="color: #333;">va</span> <span class="p">);</span> </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="3987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3987

</td>

<td class="diff-line-num new_line" data-linenumber="3994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3994

</td>

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

<pre style="margin: 0;"> <span id="LC3994" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="3988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3988

</td>

<td class="diff-line-num new_line" data-linenumber="3995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3995

</td>

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

<pre style="margin: 0;"> <span id="LC3995" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="3996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3996

</td>

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

<pre style="margin: 0;">+<span id="LC3996" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">warning_anno_vs_index</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">anno_chros_tab</span><span class="p">,</span> <span class="n" style="color: #333;">gene_offset_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">index_chros_offset</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alias_index_to_annot</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="3997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3997

</td>

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

<pre style="margin: 0;">+<span id="LC3997" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="3998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3998

</td>

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

<pre style="margin: 0;">+<span id="LC3998" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">index_chros_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index_chros_offset</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">read_name_to_index</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="3999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3999

</td>

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

<pre style="margin: 0;">+<span id="LC3999" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chros_in_annot_using_index_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">anno_chros_tab</span> <span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4000

</td>

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

<pre style="margin: 0;">+<span id="LC4000" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chros_in_index_using_annot_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index_chros_tab</span> <span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4001

</td>

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

<pre style="margin: 0;">+<span id="LC4001" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alias_annot_to_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4002

</td>

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

<pre style="margin: 0;">+<span id="LC4002" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4003

</td>

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

<pre style="margin: 0;">+<span id="LC4003" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">alias_index_to_annot</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4004

</td>

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

<pre style="margin: 0;">+<span id="LC4004" class="line" lang="c">           <span class="n" style="color: #333;">chros_in_annot_using_index_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringTableCreate</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4005

</td>

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

<pre style="margin: 0;">+<span id="LC4005" class="line" lang="c">           <span class="n" style="color: #333;">chros_in_index_using_annot_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringTableCreate</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4006

</td>

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

<pre style="margin: 0;">+<span id="LC4006" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4007

</td>

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

<pre style="margin: 0;">+<span id="LC4007" class="line" lang="c">           <span class="n" style="color: #333;">alias_annot_to_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringTableReverse</span><span class="p">(</span><span class="n" style="color: #333;">alias_index_to_annot</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4008

</td>

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

<pre style="margin: 0;">+<span id="LC4008" class="line" lang="c">           <span class="n" style="color: #333;">anno_chros_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chros_in_annot_using_index_names</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4009

</td>

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

<pre style="margin: 0;">+<span id="LC4009" class="line" lang="c">           <span class="n" style="color: #333;">anno_chros_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alias_annot_to_index</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4010

</td>

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

<pre style="margin: 0;">+<span id="LC4010" class="line" lang="c">           <span class="n" style="color: #333;">HashTableIteration</span><span class="p">(</span><span class="n" style="color: #333;">anno_chros_tab</span><span class="p">,</span> <span class="n" style="color: #333;">convert_table_key_to_alias</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4011

</td>

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

<pre style="margin: 0;">+<span id="LC4011" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4012

</td>

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

<pre style="margin: 0;">+<span id="LC4012" class="line" lang="c">           <span class="n" style="color: #333;">index_chros_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chros_in_index_using_annot_names</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4013

</td>

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

<pre style="margin: 0;">+<span id="LC4013" class="line" lang="c">           <span class="n" style="color: #333;">index_chros_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alias_index_to_annot</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4014

</td>

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

<pre style="margin: 0;">+<span id="LC4014" class="line" lang="c">           <span class="n" style="color: #333;">HashTableIteration</span><span class="p">(</span><span class="n" style="color: #333;">index_chros_tab</span><span class="p">,</span> <span class="n" style="color: #333;">convert_table_key_to_alias</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4015

</td>

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

<pre style="margin: 0;">+<span id="LC4015" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4016

</td>

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

<pre style="margin: 0;">+<span id="LC4016" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4017

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<pre style="margin: 0;">+<span id="LC4017" class="line" lang="c">   <span class="n" style="color: #333;">warning_hash_hash</span><span class="p">(</span><span class="n" style="color: #333;">anno_chros_tab</span><span class="p">,</span> <span class="n" style="color: #333;">chros_in_index_using_annot_names</span><span class="p">,</span> <span class="s" style="color: #d14;">"Chromosomes/contigs in annotation but not in index :"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4018

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

<pre style="margin: 0;">+<span id="LC4018" class="line" lang="c">   <span class="n" style="color: #333;">warning_hash_hash</span><span class="p">(</span><span class="n" style="color: #333;">index_chros_tab</span><span class="p">,</span> <span class="n" style="color: #333;">chros_in_annot_using_index_names</span><span class="p">,</span> <span class="s" style="color: #d14;">"Chromosomes/contigs in index but not in annotation :"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4019

</td>

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

<pre style="margin: 0;">+<span id="LC4019" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4020

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<pre style="margin: 0;">+<span id="LC4020" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">alias_index_to_annot</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4021

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

<pre style="margin: 0;">+<span id="LC4021" class="line" lang="c">           <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">alias_annot_to_index</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4022

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

<pre style="margin: 0;">+<span id="LC4022" class="line" lang="c">           <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">chros_in_annot_using_index_names</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4023

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

<pre style="margin: 0;">+<span id="LC4023" class="line" lang="c">           <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">chros_in_index_using_annot_names</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4024

</td>

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

<pre style="margin: 0;">+<span id="LC4024" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="3989" style="width: 35px; color: rgba(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="4025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4025

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<pre style="margin: 0;">+<span id="LC4025" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3989

</td>

<td class="diff-line-num new_line" data-linenumber="4026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4026

</td>

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

<pre style="margin: 0;"> <span id="LC4026" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3990

</td>

<td class="diff-line-num new_line" data-linenumber="4027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4027

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<pre style="margin: 0;"> <span id="LC4027" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">load_annotated_exon_regions</span><span class="p">(</span><span class="n" style="color: #333;">global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3991

</td>

<td class="diff-line-num new_line" data-linenumber="4028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4028

</td>

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

<pre style="margin: 0;"> <span id="LC4028" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bitmap_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">4096</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">EXONIC_REGION_RESOLUTION</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>

</pre>

</td>

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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="3999" style="width: 35px; color: rgba(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="4036" style="width: 35px; color: rgba(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">@@ -3999,8 +4036,6 @@ int load_annotated_exon_regions(global_context_t * global_context){</td>

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<td class="diff-line-num old_line" data-linenumber="3999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3999

</td>

<td class="diff-line-num new_line" data-linenumber="4036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4036

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<pre style="margin: 0;"> <span id="LC4036" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">loaded_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_features_annotation</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">exon_annotation_file</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">exon_annotation_file_type</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">exon_annotation_gene_id_column</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">exon_annotation_feature_name_column</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">do_anno_bitmap_add_feature</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4000

</td>

<td class="diff-line-num new_line" data-linenumber="4037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4037

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<pre style="margin: 0;"> <span id="LC4037" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">loaded_features</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span><span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4001

</td>

<td class="diff-line-num new_line" data-linenumber="4038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4038

</td>

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

<pre style="margin: 0;"> <span id="LC4038" class="line" lang="c">   <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"%d annotation records were loaded.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4002" 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">

4002

</td>

<td class="diff-line-num new_line old" data-linenumber="4039" 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="LC4002" class="line" lang="c">   <span class="n" style="color: #333;">warning_anno_vs_index</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">annotation_chro_table</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">chromosome_table</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4003" 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">

4003

</td>

<td class="diff-line-num new_line old" data-linenumber="4039" 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="LC4003" class="line" lang="c">   <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">annotation_chro_table</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4004

</td>

<td class="diff-line-num new_line" data-linenumber="4039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4039

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<pre style="margin: 0;"> <span id="LC4039" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4005

</td>

<td class="diff-line-num new_line" data-linenumber="4040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4040

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<pre style="margin: 0;"> <span id="LC4040" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4006

</td>

<td class="diff-line-num new_line" data-linenumber="4041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4041

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

<pre style="margin: 0;"> <span id="LC4041" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4021" style="width: 35px; color: rgba(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="4056" style="width: 35px; color: rgba(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">@@ -4021,9 +4056,10 @@ int load_global_context(global_context_t * context)</td>

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<td class="diff-line-num old_line" data-linenumber="4021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4021

</td>

<td class="diff-line-num new_line" data-linenumber="4056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4056

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<pre style="margin: 0;"> <span id="LC4056" class="line" lang="c">           <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">multi_best_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">multi_best_reads</span> <span class="p">,</span> <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">reported_multi_best_reads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4022

</td>

<td class="diff-line-num new_line" data-linenumber="4057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4057

</td>

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

<pre style="margin: 0;"> <span id="LC4057" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">multi_best_reads</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;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">reads_per_chunk</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">multi_best_reads</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4023

</td>

<td class="diff-line-num new_line" data-linenumber="4058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4058

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<pre style="margin: 0;"> <span id="LC4058" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="4024" style="width: 35px; color: rgba(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="4059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4059

</td>

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

<pre style="margin: 0;">+<span id="LC4059" class="line" lang="c">   <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Check the input reads."</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4024

</td>

<td class="diff-line-num new_line" data-linenumber="4060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4060

</td>

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

<pre style="margin: 0;"> <span id="LC4060" class="line" lang="c">   <span class="n" style="color: #333;">subread_init_lock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_reads</span><span class="p">.</span><span class="n" style="color: #333;">input_lock</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4025

</td>

<td class="diff-line-num new_line" data-linenumber="4061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4061

</td>

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

<pre style="margin: 0;"> <span id="LC4061" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">core_geinput_open</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_reads</span><span class="p">.</span><span class="n" style="color: #333;">first_read_file</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4026" 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">

4026

</td>

<td class="diff-line-num new_line old" data-linenumber="4062" 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>

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

<pre style="margin: 0;">-<span id="LC4026" class="line" lang="c">   <span class="idiff left">       </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//</span>sublog_printf(SUBLOG_STAGE_RELEASED, SUBLOG_LEVEL_ERROR,"Unable to open '%s' as input. Please check if it exists, you have the permission to read it, and it is in the correct format.\n", context->config.first_read_file);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4027" style="width: 35px; color: rgba(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="4062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4062

</td>

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

<pre style="margin: 0;">+<span id="LC4062" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//   </span>sublog_printf(SUBLOG_STAGE_RELEASED, SUBLOG_LEVEL_ERROR,"Unable to open '%s' as input. Please check if it exists, you have the permission to read it, and it is in the correct format.\n", context->config.first_read_file);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4027

</td>

<td class="diff-line-num new_line" data-linenumber="4063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4063

</td>

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

<pre style="margin: 0;"> <span id="LC4063" class="line" lang="c">           <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4028

</td>

<td class="diff-line-num new_line" data-linenumber="4064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4064

</td>

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

<pre style="margin: 0;"> <span id="LC4064" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4029

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<td class="diff-line-num new_line" data-linenumber="4065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4065

</td>

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

<pre style="margin: 0;"> <span id="LC4065" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4061" style="width: 35px; color: rgba(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="4097" style="width: 35px; color: rgba(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">@@ -4061,6 +4097,7 @@ int load_global_context(global_context_t * context)</td>

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<td class="diff-line-num old_line" data-linenumber="4061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4061

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<td class="diff-line-num new_line" data-linenumber="4097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4097

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<pre style="margin: 0;"> <span id="LC4097" class="line" lang="c">           <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">max_vote_number_cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4062

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<td class="diff-line-num new_line" data-linenumber="4098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4098

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<pre style="margin: 0;"> <span id="LC4098" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4063

</td>

<td class="diff-line-num new_line" data-linenumber="4099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4099

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

<pre style="margin: 0;"> <span id="LC4099" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4064" style="width: 35px; color: rgba(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="4100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4100

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

<pre style="margin: 0;">+<span id="LC4100" class="line" lang="c">   <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Initialise the memory objects."</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4064

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<td class="diff-line-num new_line" data-linenumber="4101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4101

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<pre style="margin: 0;"> <span id="LC4101" class="line" lang="c">   <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">max_vote_simples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">max_vote_simples</span> <span class="p">,</span>  <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">reported_multi_best_reads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4065

</td>

<td class="diff-line-num new_line" data-linenumber="4102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4102

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<pre style="margin: 0;"> <span id="LC4102" class="line" lang="c">   <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">max_vote_combinations</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">max_vote_combinations</span> <span class="p">,</span>  <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">reported_multi_best_reads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4066

</td>

<td class="diff-line-num new_line" data-linenumber="4103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4103

</td>

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

<pre style="margin: 0;"> <span id="LC4103" class="line" lang="c"></span>

</pre>

</td>

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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="4075" style="width: 35px; color: rgba(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="4112" style="width: 35px; color: rgba(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">@@ -4075,6 +4112,7 @@ int load_global_context(global_context_t * context)</td>

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<td class="diff-line-num old_line" data-linenumber="4075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4075

</td>

<td class="diff-line-num new_line" data-linenumber="4112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4112

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<pre style="margin: 0;"> <span id="LC4112" class="line" lang="c">   <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">first_read_file</span> <span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ginp1_stat</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4076

</td>

<td class="diff-line-num new_line" data-linenumber="4113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4113

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<pre style="margin: 0;"> <span id="LC4113" class="line" lang="c">   <span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_reads</span><span class="p">.</span><span class="n" style="color: #333;">first_read_file_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ginp1_stat</span><span class="p">.</span><span class="n" style="color: #333;">st_size</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4077

</td>

<td class="diff-line-num new_line" data-linenumber="4114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4114

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

<pre style="margin: 0;"> <span id="LC4114" class="line" lang="c"></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="4078" style="width: 35px; color: rgba(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="4115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4115

</td>

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

<pre style="margin: 0;">+<span id="LC4115" class="line" lang="c">   <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Estimate the mean read length."</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4078

</td>

<td class="diff-line-num new_line" data-linenumber="4116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4116

</td>

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

<pre style="margin: 0;"> <span id="LC4116" class="line" lang="c">   <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_reads</span><span class="p">.</span><span class="n" style="color: #333;">avg_read_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">guess_reads_density_format</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">first_read_file</span> <span class="p">,</span> <span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">is_SAM_file_input</span><span class="o" style="font-weight: 600;">?</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">min_phred_score</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_phred_score</span> <span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">guess_tested_reads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4079

</td>

<td class="diff-line-num new_line" data-linenumber="4117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4117

</td>

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

<pre style="margin: 0;"> <span id="LC4117" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_reads</span><span class="p">.</span><span class="n" style="color: #333;">avg_read_length</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;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_reads</span><span class="p">.</span><span class="n" style="color: #333;">avg_read_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">250</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4080

</td>

<td class="diff-line-num new_line" data-linenumber="4118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4118

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<pre style="margin: 0;"> <span id="LC4118" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//     SUBREADprintf("QR=[%d,%d]; ALEN=%f\n",  min_phred_score, max_phred_score, context -> input_reads.avg_read_length);</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4110" style="width: 35px; color: rgba(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="4148" style="width: 35px; color: rgba(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">@@ -4110,6 +4148,7 @@ int load_global_context(global_context_t * context)</td>

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<td class="diff-line-num old_line" data-linenumber="4110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4110

</td>

<td class="diff-line-num new_line" data-linenumber="4148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4148

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<pre style="margin: 0;"> <span id="LC4148" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;">// Only the sam file is opened here; other files like bed, indel and etc are opened in init_modules()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4111

</td>

<td class="diff-line-num new_line" data-linenumber="4149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4149

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<pre style="margin: 0;"> <span id="LC4149" class="line" lang="c">           <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tmp_fname</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">output_prefix</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4112

</td>

<td class="diff-line-num new_line" data-linenumber="4150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4150

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

<pre style="margin: 0;"> <span id="LC4150" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4113" style="width: 35px; color: rgba(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="4151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4151

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

<pre style="margin: 0;">+<span id="LC4151" class="line" lang="c">           <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Create the output %s file."</span><span class="p">,</span> <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">is_BAM_output</span><span class="o" style="font-weight: 600;">?</span><span class="s" style="color: #d14;">"BAM"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"SAM"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4113

</td>

<td class="diff-line-num new_line" data-linenumber="4152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4152

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

<pre style="margin: 0;"> <span id="LC4152" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">is_BAM_output</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4114

</td>

<td class="diff-line-num new_line" data-linenumber="4153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4153

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<pre style="margin: 0;"> <span id="LC4153" class="line" lang="c">           <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4115

</td>

<td class="diff-line-num new_line" data-linenumber="4154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4154

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<pre style="margin: 0;"> <span id="LC4154" class="line" lang="c">                   <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">output_bam_writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">SamBam_Writer</span><span class="p">));</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4140" style="width: 35px; color: rgba(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="4179" style="width: 35px; color: rgba(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">@@ -4140,6 +4179,7 @@ int load_global_context(global_context_t * context)</td>

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<td class="diff-line-num old_line" data-linenumber="4140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4140

</td>

<td class="diff-line-num new_line" data-linenumber="4179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4179

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

<pre style="margin: 0;"> <span id="LC4179" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4141

</td>

<td class="diff-line-num new_line" data-linenumber="4180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4180

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

<pre style="margin: 0;"> <span id="LC4180" class="line" lang="c">   </span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4142

</td>

<td class="diff-line-num new_line" data-linenumber="4181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4181

</td>

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

<pre style="margin: 0;"> <span id="LC4181" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">// ====== check index files, count blocks and load chro table ======</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="4143" style="width: 35px; color: rgba(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="4182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4182

</td>

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

<pre style="margin: 0;">+<span id="LC4182" class="line" lang="c">   <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Check the index."</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4143

</td>

<td class="diff-line-num new_line" data-linenumber="4183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4183

</td>

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

<pre style="margin: 0;"> <span id="LC4183" class="line" lang="c">   <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tmp_fname</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.reads"</span><span class="p">,</span> <span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">index_prefix</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4144

</td>

<td class="diff-line-num new_line" data-linenumber="4184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4184

</td>

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

<pre style="margin: 0;"> <span id="LC4184" 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;">does_file_exist</span><span class="p">(</span><span class="n" style="color: #333;">tmp_fname</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4145

</td>

<td class="diff-line-num new_line" data-linenumber="4185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4185

</td>

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

<pre style="margin: 0;"> <span id="LC4185" class="line" lang="c">   <span class="p">{</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4163" style="width: 35px; color: rgba(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="4203" style="width: 35px; color: rgba(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">@@ -4163,7 +4203,6 @@ int load_global_context(global_context_t * context)</td>

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<td class="diff-line-num old_line" data-linenumber="4163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4163

</td>

<td class="diff-line-num new_line" data-linenumber="4203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4203

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<pre style="margin: 0;"> <span id="LC4203" class="line" lang="c">           <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4164

</td>

<td class="diff-line-num new_line" data-linenumber="4204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4204

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<pre style="margin: 0;"> <span id="LC4204" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4165

</td>

<td class="diff-line-num new_line" data-linenumber="4205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4205

</td>

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

<pre style="margin: 0;"> <span id="LC4205" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4166" 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">

4166

</td>

<td class="diff-line-num new_line old" data-linenumber="4206" 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>

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

<pre style="margin: 0;">-<span id="LC4166" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4167

</td>

<td class="diff-line-num new_line" data-linenumber="4206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4206

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

<pre style="margin: 0;"> <span id="LC4206" class="line" lang="c">   <span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index_block_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4168

</td>

<td class="diff-line-num new_line" data-linenumber="4207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4207

</td>

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

<pre style="margin: 0;"> <span id="LC4207" class="line" lang="c">   <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4169

</td>

<td class="diff-line-num new_line" data-linenumber="4208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4208

</td>

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

<pre style="margin: 0;"> <span id="LC4208" class="line" lang="c">   <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4181" style="width: 35px; color: rgba(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="4220" style="width: 35px; color: rgba(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">@@ -4181,6 +4220,7 @@ int load_global_context(global_context_t * context)</td>

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<td class="diff-line-num old_line" data-linenumber="4181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4181

</td>

<td class="diff-line-num new_line" data-linenumber="4220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4220

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

<pre style="margin: 0;"> <span id="LC4220" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">report_sam_file</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4182

</td>

<td class="diff-line-num new_line" data-linenumber="4221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4221

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

<pre style="margin: 0;"> <span id="LC4221" class="line" lang="c">           <span class="n" style="color: #333;">write_sam_headers</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4183

</td>

<td class="diff-line-num new_line" data-linenumber="4222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4222

</td>

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

<pre style="margin: 0;"> <span id="LC4222" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4184" style="width: 35px; color: rgba(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="4223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4223

</td>

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

<pre style="margin: 0;">+<span id="LC4223" class="line" lang="c">   <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Init the voting space."</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4184

</td>

<td class="diff-line-num new_line" data-linenumber="4224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4224

</td>

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

<pre style="margin: 0;"> <span id="LC4224" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">// ====== init other variables ======</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4185

</td>

<td class="diff-line-num new_line" data-linenumber="4225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4225

</td>

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

<pre style="margin: 0;"> <span id="LC4225" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">all_threads</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4186

</td>

<td class="diff-line-num new_line" data-linenumber="4226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4226

</td>

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

<pre style="margin: 0;"> <span id="LC4226" class="line" lang="c">           <span class="n" style="color: #333;">subread_init_lock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">thread_initial_lock</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4197" style="width: 35px; color: rgba(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="4237" style="width: 35px; color: rgba(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">@@ -4197,10 +4237,14 @@ int load_global_context(global_context_t * context)</td>

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

<td class="diff-line-num old_line" data-linenumber="4197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4197

</td>

<td class="diff-line-num new_line" data-linenumber="4237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4237

</td>

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

<pre style="margin: 0;"> <span id="LC4237" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4198

</td>

<td class="diff-line-num new_line" data-linenumber="4238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4238

</td>

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

<pre style="margin: 0;"> <span id="LC4238" class="line" lang="c">   <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">sam_chro_to_anno_chr_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4199

</td>

<td class="diff-line-num new_line" data-linenumber="4239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4239

</td>

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

<pre style="margin: 0;"> <span id="LC4239" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">exon_annotation_file</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]){</span> </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4200" style="width: 35px; color: rgba(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="4240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4240

</td>

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

<pre style="margin: 0;">+<span id="LC4240" class="line" lang="c">           <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Load the annotation file."</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4200

</td>

<td class="diff-line-num new_line" data-linenumber="4241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4241

</td>

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

<pre style="margin: 0;"> <span id="LC4241" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">load_annotated_exon_regions</span><span class="p">(</span> <span class="n" style="color: #333;">context</span> <span class="p">)</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4201

</td>

<td class="diff-line-num new_line" data-linenumber="4242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4242

</td>

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

<pre style="margin: 0;"> <span id="LC4242" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">exon_annotation_alias_file</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4202

</td>

<td class="diff-line-num new_line" data-linenumber="4243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4243

</td>

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

<pre style="margin: 0;"> <span id="LC4243" class="line" lang="c">                    <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">sam_chro_to_anno_chr_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_alias_table</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">exon_annotation_alias_file</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="4203" style="width: 35px; color: rgba(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="4244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4244

</td>

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

<pre style="margin: 0;">+<span id="LC4244" class="line" lang="c">           <span class="n" style="color: #333;">warning_anno_vs_index</span><span class="p">(</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">annotation_chro_table</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">chromosome_table</span><span class="p">,</span> <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">sam_chro_to_anno_chr_alias</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4203" style="width: 35px; color: rgba(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="4245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4245

</td>

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

<pre style="margin: 0;">+<span id="LC4245" class="line" lang="c">           <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">annotation_chro_table</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4203

</td>

<td class="diff-line-num new_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4246

</td>

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

<pre style="margin: 0;"> <span id="LC4246" class="line" lang="c">   <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">exonic_region_bitmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="4204" style="width: 35px; color: rgba(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="4247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4247

</td>

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

<pre style="margin: 0;">+<span id="LC4247" class="line" lang="c">   <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Global environment is initialised."</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4204

</td>

<td class="diff-line-num new_line" data-linenumber="4248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4248

</td>

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

<pre style="margin: 0;"> <span id="LC4248" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4205

</td>

<td class="diff-line-num new_line" data-linenumber="4249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4249

</td>

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

<pre style="margin: 0;"> <span id="LC4249" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4206

</td>

<td class="diff-line-num new_line" data-linenumber="4250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4250

</td>

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

<pre style="margin: 0;"> <span id="LC4250" class="line" lang="c"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="3ff152fe6bda3f5dfee9715abff394de66921551">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#3ff152fe6bda3f5dfee9715abff394de66921551"><strong>src/core.h</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -204,6 +204,7 @@ typedef struct{</td>

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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

204

</td>

<td class="diff-line-num new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

204

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

<pre style="margin: 0;"> <span id="LC204" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">use_quality_score_break_ties</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

205

</td>

<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

205

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

<pre style="margin: 0;"> <span id="LC205" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">big_margin_record_size</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

206

</td>

<td class="diff-line-num new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

206

</td>

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

<pre style="margin: 0;"> <span id="LC206" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">PE_predominant_weight</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="207" style="width: 35px; color: rgba(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="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

207

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

<pre style="margin: 0;">+<span id="LC207" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">no_TLEN_preference</span><span class="p">;</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// subjunc</span></span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">entry_program_name</span><span class="p">;</span></span>

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<br>

</li>

<li id="08ec1eca3761439e06c59fe3179a2eb515dfacb1">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#08ec1eca3761439e06c59fe3179a2eb515dfacb1"><strong>src/detection-calls.c</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,8 +12,8 @@</td>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "gene-algorithms.h"</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gene_name</span><span class="p">[</span><span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span><span class="p">];</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">chro_name</span><span class="p">[</span><span class="n" style="color: #333;">MAX_CHROMOSOME_NAME_LEN</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gene_name</span><span class="p">[</span><span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">];</span></span>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">chro_name</span><span class="p">[</span><span class="n" style="color: #333;">MAX_CHROMOSOME_NAME_LEN</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">is_negative_strand</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">DTCexon_t</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(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">@@ -59,13 +59,13 @@ int DTCdo_add_feature(char * gene_name, char * transcript_name, char * chro_name</td>

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<pre style="margin: 0;"> <span id="LC59" 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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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">DTCcompare_merge_genes</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;">L_elem</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;">R_elem</span><span class="p">){</span></span>

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">DTCcompare_merge_genes</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;">L_elem</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;">R_elem</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">me</span></span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">le</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">L_elem</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">re</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_elem</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="64" style="width: 35px; color: rgba(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="LC64" class="line" lang="c">     <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">le</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">re</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(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="LC65" class="line" lang="c">     <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">le</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">re</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(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="LC66" class="line" lang="c">     <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(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="LC67" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="68" 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="LC68" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">DTCcompare_exons</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;">L_elem</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;">R_elem</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(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="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">DTCcompare_exons</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;">L_elem</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;">R_elem</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">me</span></span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(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="LC69" class="line" lang="c">     <span class="n" style="color: #333;">DTCexon_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">le</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">L_elem</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">re</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_elem</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(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="LC70" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chname_cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">le</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">chro_name</span><span class="p">,</span> <span class="n" style="color: #333;">re</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">chro_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(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="LC71" class="line" lang="c">     <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">chname_cmp</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chname_cmp</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="69742224d661e373a40a3e0ffe96a88520f33874">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#69742224d661e373a40a3e0ffe96a88520f33874"><strong>src/flattenAnnotations.c</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="145" style="width: 35px; color: rgba(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="145" style="width: 35px; color: rgba(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">@@ -145,7 +145,7 @@ int flatAnno_do_anno_1R(char * gene_name, char * transcript_name, char * chro_na</td>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">flatAnno_do_anno_merge_one_array_compare</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;">vL</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;">vR</span><span class="p">){</span></span>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(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="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">flatAnno_do_anno_merge_one_array_compare</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;">vL</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;">vR</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">me</span></span><span class="p">){</span></span>

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

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">iL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">iR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vR</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(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="LC150" 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;">iL</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;">iR</span><span class="p">))</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC151" 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;">iL</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;">iR</span><span class="p">))</span><span class="k" style="font-weight: 600;">return</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 old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -246,12 +246,16 @@ void flatAnno_do_anno_merge_one_array(void * key, void * hashed_obj, HashTable *</td>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c">    <span class="n" style="color: #333;">this_list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n1_items</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="247" style="width: 35px; color: rgba(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="LC247" class="line" lang="c"><span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="248" style="width: 35px; color: rgba(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="LC248" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="249" style="width: 35px; color: rgba(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="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">flatme_strcmp</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;">L</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;">R</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">me</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="249" style="width: 35px; color: rgba(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="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="n" style="color: #333;">R</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="249" style="width: 35px; color: rgba(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="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="249" style="width: 35px; color: rgba(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="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="253" style="width: 35px; color: rgba(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="LC253" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">flatAnno_do_anno_merge_and_write</span><span class="p">(</span><span class="n" style="color: #333;">flatAnno_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">context</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="254" style="width: 35px; color: rgba(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="LC254" class="line" lang="c">    <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">gene_chro_strand_to_exons_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">context</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="255" style="width: 35px; color: rgba(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="LC255" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c">    <span class="n" style="color: #333;">HashTableIteration</span><span class="p">(</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">gene_chro_strand_to_exons_table</span><span class="p">,</span> <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">merging_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">MERGING_MODE_CHOPPING</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">flatAnno_do_anno_chop_one_array</span> <span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">flatAnno_do_anno_merge_one_array</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="257" style="width: 35px; color: rgba(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="LC257" class="line" lang="c">    <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">all_chro_st_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableKeyArray</span><span class="p">(</span><span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">gene_chro_strand_to_exons_table</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="258" 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="LC254" class="line" lang="c">    <span class="n" style="color: #333;">ArrayListSort</span><span class="p">(</span><span class="n" style="color: #333;">all_chro_st_list</span><span class="p">,</span> <span class="p"><span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff right">))</span></span><span class="n" style="color: #333;">strcmp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="255" style="width: 35px; color: rgba(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="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c">    <span class="n" style="color: #333;">ArrayListSort</span><span class="p">(</span><span class="n" style="color: #333;">all_chro_st_list</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">flatme_</span>strcmp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="259" style="width: 35px; color: rgba(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="LC259" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="260" style="width: 35px; color: rgba(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="LC260" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">output_FP</span> <span class="p">,</span> <span class="s" style="color: #d14;">"GeneID</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Start</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">End</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Strand</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="18d5c843fdde01c811087dacdcf7dbe1f38af4d3">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#18d5c843fdde01c811087dacdcf7dbe1f38af4d3"><strong>src/gene-algorithms.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2551" style="width: 35px; color: rgba(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="2551" style="width: 35px; color: rgba(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">@@ -2551,6 +2551,7 @@ int get_base_error_prob64i(char v)</td>

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<td class="diff-line-num old_line" data-linenumber="2551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2551

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<td class="diff-line-num new_line" data-linenumber="2551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2551

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<pre style="margin: 0;"> <span id="LC2551" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PROB_QUAL_INT_TABLE</span><span class="p">[</span><span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-</span><span class="sc" style="color: #d14;">'@'</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2552

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<td class="diff-line-num new_line" data-linenumber="2552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2552

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<pre style="margin: 0;"> <span id="LC2552" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2553

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<td class="diff-line-num new_line" data-linenumber="2553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2553

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<pre style="margin: 0;"> <span id="LC2553" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2554" style="width: 35px; color: rgba(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="2554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2554" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SKIP_THIS_PART</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2555

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<pre style="margin: 0;"> <span id="LC2555" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">bad_reverse_cigar</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cigar</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2555

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<td class="diff-line-num new_line" data-linenumber="2556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2556

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<pre style="margin: 0;"> <span id="LC2556" class="line" lang="c"><span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="2556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2557" style="width: 35px; color: rgba(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="LC2557" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cigar_cursor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2600" style="width: 35px; color: rgba(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="2601" style="width: 35px; color: rgba(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">@@ -2600,6 +2601,7 @@ int debug_main()</td>

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2600

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<td class="diff-line-num new_line" data-linenumber="2601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2601

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<pre style="margin: 0;"> <span id="LC2601" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">cg</span><span class="p">);</span></span>

</pre>

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2601

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2602

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<pre style="margin: 0;"> <span id="LC2602" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2602

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2603

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<pre style="margin: 0;"> <span id="LC2603" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2604" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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2603

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<td class="diff-line-num new_line" data-linenumber="2605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2605

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<pre style="margin: 0;"> <span id="LC2605" class="line" lang="c"></span>

</pre>

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2604

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<td class="diff-line-num new_line" data-linenumber="2606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2606

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<pre style="margin: 0;"> <span id="LC2606" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">remove_indel_neighbours</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">indel_table</span><span class="p">)</span></span>

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2605

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<td class="diff-line-num new_line" data-linenumber="2607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2607

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<pre style="margin: 0;"> <span id="LC2607" class="line" lang="c"><span class="p">{</span></span>

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<br>

</li>

<li id="6612baeecf620e30ab51b9fb8e8a2afe1d40812b">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#6612baeecf620e30ab51b9fb8e8a2afe1d40812b"><strong>src/hashtable.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(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="6" style="width: 35px; color: rgba(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">@@ -6,7 +6,7 @@</td>

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Released to the public domain.</span></span>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(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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7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(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="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *--------------------------------------------------------------------------</span></span>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * $Id: hashtable.c,v 9999.<span class="idiff left right">39 2019/08/28 22:31:14</span> cvs Exp $</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * $Id: hashtable.c,v 9999.<span class="idiff left right">42 2019/12/05 03:05:37</span> cvs Exp $</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">\*--------------------------------------------------------------------------*/</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +24,7 @@ static int isProbablePrime(srInt_64 number);</td>

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

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">srInt_64</span> <span class="nf" style="color: #900; font-weight: 600;">calculateIdealNumOfBuckets</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hashTable</span><span class="p">);</span></span>

</pre>

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

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

</pre>

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

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="n" style="color: #333;">srInt_64</span> <span class="nf" style="color: #900; font-weight: 600;">long_random_val</span><span class="p">(){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">long</span></span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c">     <span class="n" style="color: #333;"><span class="idiff left right">srInt_64</span></span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c">     <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">RAND_MAX</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">255</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c">             <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Is this a embedded computer????</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="LC30" class="line" lang="c">             <span class="k" style="font-weight: 600;">return</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,6 +37,13 @@ srInt_64 long_random_val(){</td>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c">     <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListToLookupTable_Int</span><span class="p">(</span><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arr</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c">     <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">x1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c">     <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableCreate</span><span class="p">(</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">arr</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c">     <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">HashTablePut</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c">     <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"><span class="p">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"></span>

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListShift</span><span class="p">(</span><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c">     <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">elementList</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="123" style="width: 35px; color: rgba(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">@@ -116,7 +123,7 @@ void ArrayListSetDeallocationFunction(ArrayList * list,  void (*elem_deallocator</td>

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<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c">    <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">elemDeallocator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">elem_deallocator</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"><span class="p">}</span></span>

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

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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="126" 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="LC119" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListSort_comp_pntr</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;">L_elem</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;">R_elem</span> <span class="p">){</span></span>

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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListSort_comp_pntr</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;">L_elem</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;">R_elem</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">me</span></span> <span class="p">){</span></span>

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<td class="diff-line-num new_line" data-linenumber="127" style="width: 35px; color: rgba(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="LC127" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">L_elem</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">R_elem</span> <span class="p">)</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(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="LC128" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">L_elem</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">R_elem</span> <span class="p">)</span><span class="k" style="font-weight: 600;">return</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 old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(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="LC129" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" style="width: 35px; color: rgba(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="132" style="width: 35px; color: rgba(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">@@ -125,11 +132,11 @@ int ArrayListSort_comp_pntr( void * L_elem, void * R_elem ){</td>

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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(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="LC132" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListSort_compare</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;">sortdata0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">R</span><span class="p">){</span></span>

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<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(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="LC133" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">sortdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortdata0</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(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="LC134" class="line" lang="c">    <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortdata</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="135" 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="LC128" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">comp_elems</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;">L_elem</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;">R_elem</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortdata</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">comp_elems</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;">L_elem</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;">R_elem</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">me</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortdata</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(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="LC137" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">L_elem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">elementList</span><span class="p">[</span><span class="n" style="color: #333;">L</span><span class="p">];</span></span>

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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="138" style="width: 35px; color: rgba(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="LC138" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">R_elem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">elementList</span><span class="p">[</span><span class="n" style="color: #333;">R</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="139" 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="LC132" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">comp_elems</span><span class="p">(</span><span class="n" style="color: #333;">L_elem</span><span class="p">,</span> <span class="n" style="color: #333;">R_elem</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">comp_elems</span><span class="p">(</span><span class="n" style="color: #333;">L_elem</span><span class="p">,</span> <span class="n" style="color: #333;">R_elem</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">list</span></span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListSort_exchange</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;">sortdata0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">R</span><span class="p">){</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,7 +151,7 @@ void ArrayListSort_exchange(void * sortdata0, int L, int R){</td>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListSort_merge</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;">sortdata0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">items</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">items2</span><span class="p">){</span></span>

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<td class="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">sortdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortdata0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c">    <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortdata</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="154" 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="LC147" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">comp_elems</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;">L_elem</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;">R_elem</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortdata</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="148" style="width: 35px; color: rgba(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="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">comp_elems</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;">L_elem</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;">R_elem</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">me</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortdata</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"></span>

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

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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(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="LC156" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">items</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items2</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(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="LC157" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">write_cursor</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">items</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="160" style="width: 35px; color: rgba(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">@@ -153,7 +160,7 @@ void ArrayListSort_merge(void * sortdata0, int start, int items, int items2){</td>

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<td class="diff-line-num new_line" data-linenumber="160" style="width: 35px; color: rgba(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="LC160" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Elm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items</span><span class="p">)</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;">list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">elementList</span><span class="p">[</span><span class="n" style="color: #333;">read1</span><span class="p">];</span></span>

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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Elm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items2</span><span class="p">)</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;">list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">elementList</span><span class="p">[</span><span class="n" style="color: #333;">read2</span><span class="p">];</span></span>

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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="163" 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="LC156" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">select_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">:</span><span class="p">(</span> <span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">comp_elems</span><span class="p">(</span><span class="n" style="color: #333;">Elm1</span><span class="p">,</span> <span class="n" style="color: #333;">Elm2</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(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="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">select_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">:</span><span class="p">(</span> <span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">comp_elems</span><span class="p">(</span><span class="n" style="color: #333;">Elm1</span><span class="p">,</span> <span class="n" style="color: #333;">Elm2</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">list</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="164" style="width: 35px; color: rgba(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="LC164" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">select_1</span><span class="p">)</span> <span class="n" style="color: #333;">merged</span><span class="p">[</span><span class="n" style="color: #333;">write_cursor</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">elementList</span><span class="p">[</span><span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">merged</span><span class="p">[</span><span class="n" style="color: #333;">write_cursor</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">elementList</span><span class="p">[</span><span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">items2</span><span class="p">){</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(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">@@ -167,7 +174,7 @@ void ArrayListSort_merge(void * sortdata0, int start, int items, int items2){</td>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c">    <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="177" 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="LC170" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListSort</span><span class="p">(</span><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compare_L_minus_R</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;">L_elem</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;">R_elem</span><span class="p">)){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="171" style="width: 35px; color: rgba(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="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListSort</span><span class="p">(</span><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compare_L_minus_R</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;">L_elem</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;">R_elem</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">me</span></span><span class="p">)){</span></span>

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<td class="diff-line-num new_line" data-linenumber="178" style="width: 35px; color: rgba(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="LC178" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sortdata</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span>  </span>

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<td class="diff-line-num old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(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="LC179" class="line" lang="c">    <span class="n" style="color: #333;">sortdata</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="180" style="width: 35px; color: rgba(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="LC180" class="line" lang="c">    <span class="n" style="color: #333;">sortdata</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compare_L_minus_R</span><span class="o" style="font-weight: 600;">?</span><span class="n" style="color: #333;">compare_L_minus_R</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ArrayListSort_comp_pntr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="239" style="width: 35px; color: rgba(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="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -239,6 +246,21 @@ HashTable * StringTableCreate(srInt_64 numOfBuckets){</td>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="248" style="width: 35px; color: rgba(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="LC248" class="line" lang="c"></span>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">StringTableReverse_Run</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;">ky</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;">va</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tab</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="c">    <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="c">    <span class="n" style="color: #333;">HashTablePut</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">va</span><span class="p">,</span> <span class="n" style="color: #333;">ky</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">StringTableReverse</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ori</span><span class="p">){</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="c">    <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringTableCreate</span><span class="p">(</span><span class="n" style="color: #333;">ori</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfBuckets</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

256

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">oriap1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ori</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="c">    <span class="n" style="color: #333;">ori</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="c">    <span class="n" style="color: #333;">HashTableIteration</span><span class="p">(</span><span class="n" style="color: #333;">ori</span><span class="p">,</span> <span class="n" style="color: #333;">StringTableReverse_Run</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="c">    <span class="n" style="color: #333;">ori</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oriap1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(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="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

242

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<td class="diff-line-num new_line" data-linenumber="264" style="width: 35px; color: rgba(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="LC264" class="line" lang="c"><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">HashTableKeys</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tab</span><span class="p">){</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="265" style="width: 35px; color: rgba(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="LC265" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="266" style="width: 35px; color: rgba(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="LC266" class="line" lang="c">    <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListCreate</span><span class="p">(</span><span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="990" style="width: 35px; color: rgba(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="1012" style="width: 35px; color: rgba(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">@@ -990,3 +1012,34 @@ void HashTableIteration(HashTable * tab, void process_item(void * key, void * ha</td>

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<td class="diff-line-num old_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

990

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<td class="diff-line-num new_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1012

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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1013

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

<pre style="margin: 0;"> <span id="LC1013" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1014

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

<pre style="margin: 0;"> <span id="LC1014" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1015

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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">HashTableSortedIndexes_copy_idx</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;">k</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;">v</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">k2int_tab</span> <span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1017

</td>

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

<pre style="margin: 0;">+<span id="LC1017" class="line" lang="c">   <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dsta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k2int_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1018

</td>

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

<pre style="margin: 0;">+<span id="LC1018" class="line" lang="c">   <span class="n" style="color: #333;">ArrayListPush</span><span class="p">(</span><span class="n" style="color: #333;">dsta</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1019

</td>

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

<pre style="margin: 0;">+<span id="LC1019" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1020

</td>

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

<pre style="margin: 0;">+<span id="LC1020" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1021

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

<pre style="margin: 0;">+<span id="LC1021" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">HashTableSortedIndexes_cmp_idx</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;">Lv</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;">Rv</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">me</span> <span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1022

</td>

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

<pre style="margin: 0;">+<span id="LC1022" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">appdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">me</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1023

</td>

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

<pre style="margin: 0;">+<span id="LC1023" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">k2int_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">appdx</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1024

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

<pre style="margin: 0;">+<span id="LC1024" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Lhash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">k2int_tab</span><span class="p">,</span> <span class="n" style="color: #333;">Lv</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1025

</td>

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

<pre style="margin: 0;">+<span id="LC1025" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Rhash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">k2int_tab</span><span class="p">,</span> <span class="n" style="color: #333;">Rv</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1026

</td>

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

<pre style="margin: 0;">+<span id="LC1026" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">large_first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">appdx</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1027

</td>

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

<pre style="margin: 0;">+<span id="LC1027" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">large_first</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1028

</td>

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

<pre style="margin: 0;">+<span id="LC1028" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Lhash</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Rhash</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1029

</td>

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

<pre style="margin: 0;">+<span id="LC1029" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Lhash</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Rhash</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1030

</td>

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

<pre style="margin: 0;">+<span id="LC1030" class="line" lang="c">   <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1031

</td>

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

<pre style="margin: 0;">+<span id="LC1031" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Lhash</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Rhash</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1032

</td>

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

<pre style="margin: 0;">+<span id="LC1032" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Lhash</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Rhash</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1033

</td>

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

<pre style="margin: 0;">+<span id="LC1033" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1034

</td>

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

<pre style="margin: 0;">+<span id="LC1034" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1035

</td>

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

<pre style="margin: 0;">+<span id="LC1035" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1036

</td>

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

<pre style="margin: 0;">+<span id="LC1036" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1037

</td>

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

<pre style="margin: 0;">+<span id="LC1037" class="line" lang="c"><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">HashTableSortedIndexes</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">k2int_tab</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">larger_value_first</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1038

</td>

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

<pre style="margin: 0;">+<span id="LC1038" class="line" lang="c">   <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableKeys</span><span class="p">(</span><span class="n" style="color: #333;">k2int_tab</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1039

</td>

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

<pre style="margin: 0;">+<span id="LC1039" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">appx</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1040

</td>

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

<pre style="margin: 0;">+<span id="LC1040" class="line" lang="c">   <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">appx</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1041

</td>

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

<pre style="margin: 0;">+<span id="LC1041" class="line" lang="c">   <span class="n" style="color: #333;">appx</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">k2int_tab</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1042

</td>

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

<pre style="margin: 0;">+<span id="LC1042" class="line" lang="c">   <span class="n" style="color: #333;">appx</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">larger_value_first</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1043

</td>

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

<pre style="margin: 0;">+<span id="LC1043" class="line" lang="c">   <span class="n" style="color: #333;">ArrayListSort</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">HashTableSortedIndexes_cmp_idx</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1044

</td>

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

<pre style="margin: 0;">+<span id="LC1044" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="993" style="width: 35px; color: rgba(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="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1045

</td>

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

<pre style="margin: 0;">+<span id="LC1045" class="line" lang="c"><span class="p">}</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="30c07b024c4fcae2a43837631bde802ba5d8e371">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#30c07b024c4fcae2a43837631bde802ba5d8e371"><strong>src/hashtable.h</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(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="6" style="width: 35px; color: rgba(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">@@ -6,7 +6,7 @@</td>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Released to the public domain.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

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

<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

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

<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *--------------------------------------------------------------------------</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * $Id: hashtable.h,v 9999.<span class="idiff left right">27 2019/08/25 10:12:06</span> cvs Exp $</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * $Id: hashtable.h,v 9999.<span class="idiff left right">30 2019/12/05 03:05:37</span> cvs Exp $</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">\*--------------------------------------------------------------------------*/</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef _HASHTABLE_H</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,7 +71,7 @@ int ArrayListPush_NoRepeatedPtr(ArrayList * list, void * new_elem);</td>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListShift</span><span class="p">(</span><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListPop</span><span class="p">(</span><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListSetDeallocationFunction</span><span class="p">(</span><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span>  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">elem_deallocator</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;">elem</span><span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListSort</span><span class="p">(</span><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compare_L_minus_R</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;">L_elem</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;">R_elem</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListSort</span><span class="p">(</span><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compare_L_minus_R</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;">L_elem</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;">R_elem</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">me</span></span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// A simple comparison function if you want to sort unsigned long long ints.</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListLLUComparison</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;">L_elem</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;">R_elem</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -115,6 +115,7 @@ ArrayList * HashTableKeyArray(HashTable * tab);</td>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">\*--------------------------------------------------------------------------*/</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">StringTableCreate</span><span class="p">(</span><span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">numOfBuckets</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">StringTableReverse</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ori</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">HashTableCreate</span><span class="p">(</span><span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">numOfBuckets</span><span class="p">);</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*--------------------------------------------------------------------------*\</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -494,6 +495,11 @@ srUInt_64 HashTableStringHashFunction(const void *key);</td>

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">free_values_destroy</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tab</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">HashTablePutReplaceEx</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hashTable</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</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;">key</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;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">replace_key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dealloc_key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dealloc_value</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="c"><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">HashTableSortedIndexes</span><span class="p">(</span><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">k2int_tab</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">larger_value_first</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// NOTE: values are all added by 1. </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ArrayListToLookupTable_Int</span><span class="p">(</span><span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arr</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC503" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif </span><span class="cm" style="color: #998; font-style: italic;">/* _HASHTABLE_H */</span></span>

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<pre style="margin: 0;"> <span id="LC504" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="c"></span></pre>

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<li id="db883abc086707d455e41cc6745055f2475bcc7f">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#db883abc086707d455e41cc6745055f2475bcc7f"><strong>src/index-builder.c</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -441,31 +441,25 @@ int build_gene_index(const char index_prefix [], char ** chro_files, int chro_fi</td>

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<pre style="margin: 0;"> <span id="LC441" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">add_repeated_subread</span><span class="p">(</span><span class="n" style="color: #333;">gehash_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tab</span> <span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">subr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">huge_index</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="c"><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC444" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">huge_byte</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">subr</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="mh" style="color: #099;"><span class="idiff right">0x3fffffff</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC445" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">huge_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">subr</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;"><span class="idiff left">4</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC446" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ind_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">huge_byte</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2<span class="idiff left">0</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1023</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">huge_byte</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">subr</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">huge_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">subr</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">4</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ind_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">huge_byte</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2<span class="idiff left">4</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">127</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC448" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">ind_id</span><span class="p">])</span>  <span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">ind_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC449" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">ind_id</span><span class="p">]){</span> </span>

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<pre style="margin: 0;">-<span id="LC450" class="line" lang="c">            <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: No memory can be allocated.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">The program has to terminate</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="LC451" class="line" lang="c">            <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC452" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="453" 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">

453

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<td class="diff-line-num new_line old" data-linenumber="448" 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="LC453" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">byte_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">huge_index</span><span class="p">[</span> <span class="n" style="color: #333;">ind_id</span> <span class="p">][</span><span class="n" style="color: #333;">huge_byte</span><span class="o" style="font-weight: 600;">&</span><span class="mh" style="color: #099;">0xfffff</span><span class="p">]</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="454" style="width: 35px; color: rgba(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="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

448

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">byte_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">huge_index</span><span class="p">[</span> <span class="n" style="color: #333;">ind_id</span> <span class="p">][</span><span class="n" style="color: #333;">huge_byte</span><span class="o" style="font-weight: 600;">&</span><span class="mh" style="color: #099;">0xffffff</span><span class="p">]</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

454

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<td class="diff-line-num new_line" data-linenumber="449" style="width: 35px; color: rgba(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="LC449" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="455" 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">

455

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<td class="diff-line-num new_line old" data-linenumber="450" 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="LC455" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">huge_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">byte_value</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">huge_offset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x<span class="idiff left right">3</span></span><span class="p">;</span></span>

</pre>

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456

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<td class="diff-line-num new_line old" data-linenumber="450" 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="LC456" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">huge_value</span> <span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;"><span class="idiff left right">3</span></span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="457" style="width: 35px; color: rgba(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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450

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

<pre style="margin: 0;">+<span id="LC450" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">huge_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">byte_value</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">huge_offset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x<span class="idiff left right">f</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="457" style="width: 35px; color: rgba(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="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

451

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">huge_value</span> <span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;"><span class="idiff left right">15</span></span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

457

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452

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="c">            <span class="n" style="color: #333;">huge_value</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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458

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<td class="diff-line-num new_line old" data-linenumber="453" 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="LC458" class="line" lang="c">            <span class="n" style="color: #333;">huge_index</span><span class="p">[</span> <span class="n" style="color: #333;">ind_id</span> <span class="p">][</span><span class="n" style="color: #333;">huge_byte</span><span class="o" style="font-weight: 600;">&</span><span class="mh" style="color: #099;">0xfffff</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">byte_value</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">~</span><span class="p">(</span><span class="mh" style="color: #099;">0x3</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">huge_offset</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">huge_value</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">huge_offset</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="c">            <span class="n" style="color: #333;">byte_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">byte_value</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">~</span><span class="p">(</span><span class="mh" style="color: #099;">0xf</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">huge_offset</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">huge_value</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">huge_offset</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="459" style="width: 35px; color: rgba(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="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="c">            <span class="n" style="color: #333;">huge_index</span><span class="p">[</span> <span class="n" style="color: #333;">ind_id</span> <span class="p">][</span><span class="n" style="color: #333;">huge_byte</span><span class="o" style="font-weight: 600;">&</span><span class="mh" style="color: #099;">0xffffff</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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)(</span><span class="n" style="color: #333;">byte_value</span><span class="o" style="font-weight: 600;">&</span><span class="mh" style="color: #099;">0xff</span><span class="p">);</span></span>

</pre>

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459

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<td class="diff-line-num new_line" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

455

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="c">            <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

460

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<td class="diff-line-num new_line" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

456

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

461

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<td class="diff-line-num new_line" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">times</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

462

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">matched</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gehash_get</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">,</span> <span class="n" style="color: #333;">subr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">times</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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463

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459

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">matched</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC464" class="line" lang="c">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

465

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="c">            <span class="n" style="color: #333;">gehash_update</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">,</span> <span class="n" style="color: #333;">subr</span><span class="p">,</span> <span class="n" style="color: #333;">times</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="461" 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="LC466" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

467

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span></span>

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<td class="diff-line-num old old_line" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="462" 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="LC468" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gehash_insert</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">,</span> <span class="n" style="color: #333;">subr</span><span class="p">,</span><span class="mi" style="color: #099;"><span class="idiff left right">4</span></span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gehash_insert</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">,</span> <span class="n" style="color: #333;">subr</span><span class="p">,</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff right">16</span></span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC463" class="line" lang="c">    </span>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

471

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="480" style="width: 35px; color: rgba(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="474" style="width: 35px; color: rgba(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">@@ -480,26 +474,17 @@ int scan_gene_index(const char index_prefix [], char ** chro_files, int chro_fil</td>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="c">    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">actual_total_bases_inc_marging</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">padding_around_contigs</span><span class="p">;</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="c">    <span class="n" style="color: #333;">gehash_t</span> <span class="n" style="color: #333;">occurrence_table</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="477" 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="LC483" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="mi" style="color: #099;">1024</span><span class="p">];</span></span>

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<td class="diff-line-num new_line old" data-linenumber="477" 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="LC484" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="477" 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="LC485" 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="mi" style="color: #099;">1024</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="486" 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="LC486" class="line" lang="c">    <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="487" 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">

487

</td>

<td class="diff-line-num new_line old" data-linenumber="477" 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="LC487" class="line" lang="c">            <span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="488" style="width: 35px; color: rgba(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="477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

477

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="mi" style="color: #099;">128</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

488

</td>

<td class="diff-line-num new_line" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

478

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

<pre style="margin: 0;"> <span id="LC478" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="489" 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">

489

</td>

<td class="diff-line-num new_line old" data-linenumber="479" 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="LC489" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="c1" style="color: #998; font-style: italic;">//memory is allocated when needed. </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="490" 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">

490

</td>

<td class="diff-line-num new_line old" data-linenumber="479" 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="LC490" class="line" lang="c">                    <span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p">);</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="491" 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">

491

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<td class="diff-line-num new_line old" data-linenumber="479" 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="LC491" class="line" lang="c">                    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="492" 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">

492

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<td class="diff-line-num new_line old" data-linenumber="479" 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="LC492" 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;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="493" 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">

493

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<td class="diff-line-num new_line old" data-linenumber="479" 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="LC493" class="line" lang="c">                    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="494" 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">

494

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<td class="diff-line-num new_line old" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC494" class="line" lang="c">                            <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">i</span><span class="p">;</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="495" 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">

495

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<td class="diff-line-num new_line old" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC495" class="line" lang="c">                            <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: You need at least one point five gigabytes of memory for building the index.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="496" 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">

496

</td>

<td class="diff-line-num new_line old" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC496" class="line" lang="c">                            <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="497" 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">

497

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<td class="diff-line-num new_line old" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC497" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="498" 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">

498

</td>

<td class="diff-line-num new_line old" data-linenumber="479" 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>

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

<pre style="margin: 0;">-<span id="LC498" class="line" lang="c">                    <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span> <span class="p">,</span> <span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="499" style="width: 35px; color: rgba(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="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

479

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

<pre style="margin: 0;">+<span id="LC479" 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="mi" style="color: #099;">128</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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="499" style="width: 35px; color: rgba(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="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

480

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

<pre style="margin: 0;">+<span id="LC480" class="line" lang="c">            <span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">16</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="499" style="width: 35px; color: rgba(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="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

481

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

<pre style="margin: 0;">+<span id="LC481" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]){</span> </span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="499" style="width: 35px; color: rgba(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="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

482

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="c">                    <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: No memory can be allocated.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">The program has to terminate</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="499" style="width: 35px; color: rgba(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="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

483

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="c">                    <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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

499

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<td class="diff-line-num new_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

484

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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

500

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<td class="diff-line-num new_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

485

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<pre style="margin: 0;"> <span id="LC485" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

501

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<td class="diff-line-num new_line" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

486

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="502" 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">

502

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<td class="diff-line-num new_line old" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC502" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gehash_create_ex</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">occurrence_table</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">1500</span>00000</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

487

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gehash_create_ex</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">occurrence_table</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">5</span>00000</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

503

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<td class="diff-line-num new_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

488

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

<pre style="margin: 0;"> <span id="LC488" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

504

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<td class="diff-line-num new_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

489

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="c">    <span class="n" style="color: #333;">gene_input_t</span> <span class="n" style="color: #333;">ginp</span><span class="p">;</span></span>

</pre>

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

505

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

490

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

<pre style="margin: 0;"> <span id="LC490" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="677" style="width: 35px; color: rgba(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="662" style="width: 35px; color: rgba(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">@@ -677,7 +662,7 @@ int scan_gene_index(const char index_prefix [], char ** chro_files, int chro_fil</td>

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677

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<td class="diff-line-num new_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

662

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

678

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<td class="diff-line-num new_line" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

663

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

<pre style="margin: 0;"> <span id="LC663" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

679

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<td class="diff-line-num new_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

664

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

<pre style="margin: 0;"> <span id="LC664" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="680" 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">

680

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<td class="diff-line-num new_line old" data-linenumber="665" 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>

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

<pre style="margin: 0;">-<span id="LC680" 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="mi" style="color: #099;">1<span class="idiff left right">024</span></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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="681" style="width: 35px; color: rgba(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="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

665

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

<pre style="margin: 0;">+<span id="LC665" 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="mi" style="color: #099;">1<span class="idiff left right">28</span></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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

681

</td>

<td class="diff-line-num new_line" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

666

</td>

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

<pre style="margin: 0;"> <span id="LC666" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span>  <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">huge_index</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

682

</td>

<td class="diff-line-num new_line" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

667

</td>

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

<pre style="margin: 0;"> <span id="LC667" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

683

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<td class="diff-line-num new_line" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

668

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="c">    <span class="n" style="color: #333;">gehash_destory</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">occurrence_table</span><span class="p">);</span></span>

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<li id="af240e90f84ee342e36f1a8ee0eb08f1a4b16a3d">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#af240e90f84ee342e36f1a8ee0eb08f1a4b16a3d"><strong>src/input-files.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2544" style="width: 35px; color: rgba(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="2544" style="width: 35px; color: rgba(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">@@ -2544,7 +2544,8 @@ int SAM_pairer_create(SAM_pairer_context_t * pairer, int all_threads, int bin_bu</td>

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<pre style="margin: 0;"> <span id="LC2544" class="line" lang="c">           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">].</span><span class="n" style="color: #333;">thread_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC2545" class="line" lang="c">           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">].</span><span class="n" style="color: #333;">reads_in_SBAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC2546" class="line" lang="c">           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">].</span><span class="n" style="color: #333;">input_buff_SBAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_SBAM_size</span><span class="p">);</span></span>

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2547

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<td class="diff-line-num new_line old" data-linenumber="2547" 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="LC2547" class="line" lang="c">           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">].</span><span class="n" style="color: #333;">input_buff_BIN</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_size</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="2548" style="width: 35px; color: rgba(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="2547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2547" class="line" lang="c">           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">].</span><span class="n" style="color: #333;">input_buff_BIN_capacity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_size</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2548" style="width: 35px; color: rgba(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="2548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2548" class="line" lang="c">           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">].</span><span class="n" style="color: #333;">input_buff_BIN</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">].</span><span class="n" style="color: #333;">input_buff_BIN_capacity</span> <span class="p">);</span></span>

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2548

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2549

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<pre style="margin: 0;"> <span id="LC2549" class="line" lang="c"></span>

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2549

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<td class="diff-line-num new_line" data-linenumber="2550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2550

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<pre style="margin: 0;"> <span id="LC2550" class="line" lang="c">           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">].</span><span class="n" style="color: #333;">input_buff_BIN_used</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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2550

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<td class="diff-line-num new_line" data-linenumber="2551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2551

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<pre style="margin: 0;"> <span id="LC2551" class="line" lang="c">           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">].</span><span class="n" style="color: #333;">orphant_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableCreate</span><span class="p">(</span><span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_SBAM_size</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2615" style="width: 35px; color: rgba(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="2616" style="width: 35px; color: rgba(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">@@ -2615,7 +2616,7 @@ int SAM_pairer_read_BAM_block(FILE * fp, int max_read_len, char * inbuff) {</td>

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2615

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<td class="diff-line-num new_line" data-linenumber="2616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2616

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<pre style="margin: 0;"> <span id="LC2616" class="line" lang="c">           <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="2617" style="width: 35px; color: rgba(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="LC2617" class="line" lang="c">   <span class="p">}</span></span>

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2617

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<td class="diff-line-num new_line" data-linenumber="2618" style="width: 35px; color: rgba(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="LC2618" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gz_header_12</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">31</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">gz_header_12</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">139</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC2618" class="line" lang="c">           <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized Gzip headers: %u, %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Please make sure if the input file is in the BAM format.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">gz_header_12</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">gz_header_12</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2619" style="width: 35px; color: rgba(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="2619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2619" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>SUBREADprintf("Unrecognized Gzip headers: %u, %u\nPlease make sure if the input file is in the BAM format.\n", gz_header_12[0], gz_header_12[1]);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2619

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<td class="diff-line-num new_line" data-linenumber="2620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2620

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<pre style="margin: 0;"> <span id="LC2620" class="line" lang="c">           <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2621

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<pre style="margin: 0;"> <span id="LC2621" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2621

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<td class="diff-line-num new_line" data-linenumber="2622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2622

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<pre style="margin: 0;"> <span id="LC2622" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">xlen</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;">bsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2768" style="width: 35px; color: rgba(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="2769" style="width: 35px; color: rgba(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">@@ -2768,16 +2769,31 @@ int SAM_pairer_fetch_BAM_block(SAM_pairer_context_t * pairer , SAM_pairer_thread</td>

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<td class="diff-line-num old_line" data-linenumber="2768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2768

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<td class="diff-line-num new_line" data-linenumber="2769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2769

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<pre style="margin: 0;"> <span id="LC2769" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2770

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<pre style="margin: 0;"> <span id="LC2770" class="line" lang="c">   <span class="n" style="color: #333;">inflateReset</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">strm</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2770

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<td class="diff-line-num new_line" data-linenumber="2771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2771

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

<pre style="margin: 0;"> <span id="LC2771" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2771" 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">

2771

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<td class="diff-line-num new_line old" data-linenumber="2772" 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="LC2771" class="line" lang="c">   <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_SBAM_used</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_SBAM_ptr</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2772" style="width: 35px; color: rgba(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="2772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2772

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<pre style="margin: 0;">+<span id="LC2772" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lin</span><span class="p">,</span> <span class="n" style="color: #333;">lout</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2772" style="width: 35px; color: rgba(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="2773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2773

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

<pre style="margin: 0;">+<span id="LC2773" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2772" style="width: 35px; color: rgba(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="2774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2774

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<pre style="margin: 0;">+<span id="LC2774" class="line" lang="c">   <span class="n" style="color: #333;">lin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_SBAM_used</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_SBAM_ptr</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2775" style="width: 35px; color: rgba(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="LC2775" class="line" lang="c">   <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_SBAM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_SBAM_ptr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2773" 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">

2773

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<td class="diff-line-num new_line old" data-linenumber="2776" 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="LC2773" class="line" lang="c">   <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_used</span><span class="p">;</span> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2776

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<pre style="margin: 0;">+<span id="LC2776" class="line" lang="c">   </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2777

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<pre style="margin: 0;">+<span id="LC2777" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_capacity</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_used</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">128</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2778

</td>

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

<pre style="margin: 0;">+<span id="LC2778" class="line" lang="c">           <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_capacity</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_used</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_capacity</span> <span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2779

</td>

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

<pre style="margin: 0;">+<span id="LC2779" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_capacity</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p">){</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2780

</td>

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

<pre style="margin: 0;">+<span id="LC2780" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: buffer size larger than 1GB</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2781

</td>

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

<pre style="margin: 0;">+<span id="LC2781" class="line" lang="c">                   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2782

</td>

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

<pre style="margin: 0;">+<span id="LC2782" class="line" lang="c">           <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2783

</td>

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

<pre style="margin: 0;">+<span id="LC2783" class="line" lang="c">                   <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("Resize Buffer of Th_%d to %d (used %d); In_ava=%d - %d\n", thread_context -> thread_id,  thread_context -> input_buff_BIN_capacity, thread_context -> input_buff_BIN_used, thread_context -> input_buff_SBAM_used , thread_context -> input_buff_SBAM_ptr);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2784

</td>

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

<pre style="margin: 0;">+<span id="LC2784" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2785

</td>

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

<pre style="margin: 0;">+<span id="LC2785" class="line" lang="c">           <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">realloc</span><span class="p">(</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN</span> <span class="p">,</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_capacity</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2786

</td>

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

<pre style="margin: 0;">+<span id="LC2786" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("  PTR=%p\n",thread_context -> input_buff_BIN);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2787

</td>

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

<pre style="margin: 0;">+<span id="LC2787" class="line" lang="c">           <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2788

</td>

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

<pre style="margin: 0;">+<span id="LC2788" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2774" style="width: 35px; color: rgba(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="2789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2789

</td>

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

<pre style="margin: 0;">+<span id="LC2789" class="line" lang="c">   <span class="n" style="color: #333;">lout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_capacity</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_used</span><span class="p">;</span> </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2774

</td>

<td class="diff-line-num new_line" data-linenumber="2790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2790

</td>

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

<pre style="margin: 0;"> <span id="LC2790" class="line" lang="c">   <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">next_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_used</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="2775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2775

</td>

<td class="diff-line-num new_line" data-linenumber="2791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2791

</td>

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

<pre style="margin: 0;"> <span id="LC2791" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2776

</td>

<td class="diff-line-num new_line" data-linenumber="2792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2792

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<pre style="margin: 0;"> <span id="LC2792" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inflate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strm</span><span class="p">,</span> <span class="n" style="color: #333;">Z_FINISH</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2777

</td>

<td class="diff-line-num new_line" data-linenumber="2793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2793

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<pre style="margin: 0;"> <span id="LC2793" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Z_OK</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Z_STREAM_END</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2778

</td>

<td class="diff-line-num new_line" data-linenumber="2794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2794

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<pre style="margin: 0;"> <span id="LC2794" class="line" lang="c">   <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2779" 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">

2779

</td>

<td class="diff-line-num new_line old" data-linenumber="2795" 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="LC2779" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">have</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">pairer</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">input_buff_BIN_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">thread_context</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">strm</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">avail_out</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">thread_context</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">input_buff_BIN_used</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2780" 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">

2780

</td>

<td class="diff-line-num new_line old" data-linenumber="2795" 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="LC2780" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">used_BAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">thread_context</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">input_buff_SBAM_used</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">thread_context</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">input_buff_SBAM_ptr</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2781" style="width: 35px; color: rgba(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="2795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2795

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

<pre style="margin: 0;">+<span id="LC2795" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">have</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">lout</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">thread_context</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">strm</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">avail_out</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2781" style="width: 35px; color: rgba(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="2796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2796

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<pre style="margin: 0;">+<span id="LC2796" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">used_BAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">lin</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2781

</td>

<td class="diff-line-num new_line" data-linenumber="2797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2797

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<pre style="margin: 0;"> <span id="LC2797" class="line" lang="c">           </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2782

</td>

<td class="diff-line-num new_line" data-linenumber="2798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2798

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<pre style="margin: 0;"> <span id="LC2798" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("ABBO TH %d : INFLATED BAM_CONSUMED: %d BIN_USED: %d => %d    NEED_FIND_START=%d\n", thread_context -> thread_id, used_BAM, thread_context -> input_buff_BIN_used , thread_context -> input_buff_BIN_used+have, thread_context -> need_find_start);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2783

</td>

<td class="diff-line-num new_line" data-linenumber="2799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2799

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

<pre style="margin: 0;"> <span id="LC2799" class="line" lang="c">           <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_used</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">have</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2785" style="width: 35px; color: rgba(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="2801" style="width: 35px; color: rgba(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">@@ -2785,16 +2801,24 @@ int SAM_pairer_fetch_BAM_block(SAM_pairer_context_t * pairer , SAM_pairer_thread</td>

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<td class="diff-line-num old_line" data-linenumber="2785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2785

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<td class="diff-line-num new_line" data-linenumber="2801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2801

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

<pre style="margin: 0;"> <span id="LC2801" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2786

</td>

<td class="diff-line-num new_line" data-linenumber="2802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2802

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<pre style="margin: 0;"> <span id="LC2802" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">need_find_start</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2787

</td>

<td class="diff-line-num new_line" data-linenumber="2803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2803

</td>

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

<pre style="margin: 0;"> <span id="LC2803" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">test_read_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAM_pairer_find_start</span><span class="p">(</span><span class="n" style="color: #333;">pairer</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2788" 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">

2788

</td>

<td class="diff-line-num new_line old" data-linenumber="2804" 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="LC2788" class="line" lang="c">                   <span class="c1" style="color: #998; font-style: italic;">//#warning "====================== FOR TESTINg FALL BACK ONLY, MUST REMOVE FROM RELEASE ============================"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2789

</td>

<td class="diff-line-num new_line" data-linenumber="2804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2804

</td>

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

<pre style="margin: 0;"> <span id="LC2804" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">test_read_bin</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_used</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">32</span>  <span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2790

</td>

<td class="diff-line-num new_line" data-linenumber="2805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2805

</td>

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

<pre style="margin: 0;"> <span id="LC2805" class="line" lang="c">                           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_bad_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="2791" 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">

2791

</td>

<td class="diff-line-num new_line old" data-linenumber="2806" 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>

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

<pre style="margin: 0;">-<span id="LC2791" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("ABBO : BAD_FMT 01\n");</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2792" style="width: 35px; color: rgba(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="2806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2806

</td>

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

<pre style="margin: 0;">+<span id="LC2806" class="line" lang="c">                   <span class="c1" style="color: #998; font-style: italic;">//  #warning "BADFORMAT-DEBUG"</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2792" style="width: 35px; color: rgba(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="2807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2807

</td>

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

<pre style="margin: 0;">+<span id="LC2807" class="line" lang="c">                   <span class="c1" style="color: #998; font-style: italic;">//  SUBREADprintf("ABBO : BAD_FMT 01\n");</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2792

</td>

<td class="diff-line-num new_line" data-linenumber="2808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2808

</td>

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

<pre style="margin: 0;"> <span id="LC2808" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2793

</td>

<td class="diff-line-num new_line" data-linenumber="2809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2809

</td>

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

<pre style="margin: 0;"> <span id="LC2809" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2794" style="width: 35px; color: rgba(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="2810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2810

</td>

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

<pre style="margin: 0;">+<span id="LC2810" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("FETCHED BLOCK DECOMP=%d FROM COMP=%d\n", have, used_BAM);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2794

</td>

<td class="diff-line-num new_line" data-linenumber="2811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2811

</td>

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

<pre style="margin: 0;"> <span id="LC2811" class="line" lang="c">   <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="2795" 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">

2795

</td>

<td class="diff-line-num new_line old" data-linenumber="2812" 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>

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

<pre style="margin: 0;">-<span id="LC2795" class="line" lang="c">           <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"GZIP ERROR:%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">ret</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2796" style="width: 35px; color: rgba(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="2812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2812

</td>

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

<pre style="margin: 0;">+<span id="LC2812" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2796" style="width: 35px; color: rgba(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="2813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2813

</td>

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

<pre style="margin: 0;">+<span id="LC2813" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot parse the input BAM file. If the BAM file contains long reads, please run featureCounts on the long-read mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2796" style="width: 35px; color: rgba(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="2814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2814

</td>

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

<pre style="margin: 0;">+<span id="LC2814" class="line" lang="c">           <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2796" style="width: 35px; color: rgba(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="2815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2815

</td>

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

<pre style="margin: 0;">+<span id="LC2815" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"GZIP ERROR:%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">ret</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2796" style="width: 35px; color: rgba(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="2816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2816

</td>

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

<pre style="margin: 0;">+<span id="LC2816" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2796" style="width: 35px; color: rgba(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="2817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2817

</td>

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

<pre style="margin: 0;">+<span id="LC2817" class="line" lang="c">           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_bad_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2796" style="width: 35px; color: rgba(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="2818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2818

</td>

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

<pre style="margin: 0;">+<span id="LC2818" class="line" lang="c">           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_internal_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2796

</td>

<td class="diff-line-num new_line" data-linenumber="2819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2819

</td>

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

<pre style="margin: 0;"> <span id="LC2819" class="line" lang="c">           <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2797

</td>

<td class="diff-line-num new_line" data-linenumber="2820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2820

</td>

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

<pre style="margin: 0;"> <span id="LC2820" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2798" style="width: 35px; color: rgba(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="2821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2821

</td>

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

<pre style="margin: 0;">+<span id="LC2821" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2798

</td>

<td class="diff-line-num new_line" data-linenumber="2822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2822

</td>

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

<pre style="margin: 0;"> <span id="LC2822" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2799

</td>

<td class="diff-line-num new_line" data-linenumber="2823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2823

</td>

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

<pre style="margin: 0;"> <span id="LC2823" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2800

</td>

<td class="diff-line-num new_line" data-linenumber="2824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2824

</td>

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

<pre style="margin: 0;"> <span id="LC2824" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2834" style="width: 35px; color: rgba(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="2858" style="width: 35px; color: rgba(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">@@ -2834,7 +2858,7 @@ void SAM_pairer_reduce_BAM_bin(SAM_pairer_context_t * pairer, SAM_pairer_thread_</td>

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

<td class="diff-line-num old_line" data-linenumber="2834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2834

</td>

<td class="diff-line-num new_line" data-linenumber="2858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2858

</td>

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

<pre style="margin: 0;"> <span id="LC2858" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2835

</td>

<td class="diff-line-num new_line" data-linenumber="2859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2859

</td>

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

<pre style="margin: 0;"> <span id="LC2859" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2836

</td>

<td class="diff-line-num new_line" data-linenumber="2860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2860

</td>

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

<pre style="margin: 0;"> <span id="LC2860" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="2837" 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">

2837

</td>

<td class="diff-line-num new_line old" data-linenumber="2861" 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="LC2837" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_BIN_RECORD_LENGTH ( 24*1024)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2838" style="width: 35px; color: rgba(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="2861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2861

</td>

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

<pre style="margin: 0;">+<span id="LC2861" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_BIN_RECORD_LENGTH ( 2<span class="idiff left right">0*102</span>4*1024)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2838

</td>

<td class="diff-line-num new_line" data-linenumber="2862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2862

</td>

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

<pre style="margin: 0;"> <span id="LC2862" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">reduce_SAM_to_BAM</span><span class="p">(</span><span class="n" style="color: #333;">SAM_pairer_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pairer</span> <span class="p">,</span> <span class="n" style="color: #333;">SAM_pairer_thread_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">thread_context</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">include_sequence</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2839

</td>

<td class="diff-line-num new_line" data-linenumber="2863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2863

</td>

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

<pre style="margin: 0;"> <span id="LC2863" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">is_read_bin</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bin</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bin_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_refID</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2840

</td>

<td class="diff-line-num new_line" data-linenumber="2864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2864

</td>

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

<pre style="margin: 0;"> <span id="LC2864" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2886" style="width: 35px; color: rgba(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="2910" style="width: 35px; color: rgba(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">@@ -2886,7 +2910,8 @@ int SAM_pairer_get_next_read_BIN( SAM_pairer_context_t * pairer , SAM_pairer_thr</td>

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

<td class="diff-line-num old_line" data-linenumber="2886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2886

</td>

<td class="diff-line-num new_line" data-linenumber="2910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2910

</td>

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

<pre style="margin: 0;"> <span id="LC2910" class="line" lang="c">                                   <span class="n" style="color: #333;">ref_bin_len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="2887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2887

</td>

<td class="diff-line-num new_line" data-linenumber="2911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2911

</td>

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

<pre style="margin: 0;"> <span id="LC2911" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2888

</td>

<td class="diff-line-num new_line" data-linenumber="2912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2912

</td>

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

<pre style="margin: 0;"> <span id="LC2912" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="2889" 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">

2889

</td>

<td class="diff-line-num new_line old" data-linenumber="2913" 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>

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

<pre style="margin: 0;">-<span id="LC2889" class="line" lang="c">                           <span class="n" style="color: #333;">is_OK</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_OK</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">output_header</span><span class="p">(</span><span class="n" style="color: #333;">pairer</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">thread_id</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">BAM_n_ref</span> <span class="p">,</span> <span class="n" style="color: #333;">header_txt</span> <span class="p">,</span> <span class="n" style="color: #333;">ref_bin_len</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2890" style="width: 35px; color: rgba(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="2913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2913

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<pre style="margin: 0;">+<span id="LC2913" class="line" lang="c">                           <span class="n" style="color: #333;">is_OK</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_OK</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">output_header</span><span class="p">(</span><span class="n" style="color: #333;">pairer</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">thread_id</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">BAM_n_ref</span> <span class="p">,</span> <span class="n" style="color: #333;">header_txt</span> <span class="p">,</span>  <span class="n" style="color: #333;">ref_bin_len</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2890" style="width: 35px; color: rgba(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="2914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2914

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<pre style="margin: 0;">+<span id="LC2914" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("TFMT:HEADER REFS=%d TXTS=%d SIGN=%u\n", pairer -> BAM_n_ref, pairer->BAM_l_text, bam_signature);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2890

</td>

<td class="diff-line-num new_line" data-linenumber="2915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2915

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<pre style="margin: 0;"> <span id="LC2915" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2891

</td>

<td class="diff-line-num new_line" data-linenumber="2916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2916

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<pre style="margin: 0;"> <span id="LC2916" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">header_txt</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">header_txt</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2892

</td>

<td class="diff-line-num new_line" data-linenumber="2917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2917

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<pre style="margin: 0;"> <span id="LC2917" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">is_OK</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2895" style="width: 35px; color: rgba(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="2920" style="width: 35px; color: rgba(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">@@ -2895,11 +2920,7 @@ int SAM_pairer_get_next_read_BIN( SAM_pairer_context_t * pairer , SAM_pairer_thr</td>

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<td class="diff-line-num old_line" data-linenumber="2895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2895

</td>

<td class="diff-line-num new_line" data-linenumber="2920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2920

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<pre style="margin: 0;"> <span id="LC2920" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2896

</td>

<td class="diff-line-num new_line" data-linenumber="2921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2921

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

<pre style="margin: 0;"> <span id="LC2921" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2897

</td>

<td class="diff-line-num new_line" data-linenumber="2922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2922

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<pre style="margin: 0;"> <span id="LC2922" class="line" lang="c">                           <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">BAM_header_parsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2898" 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">

2898

</td>

<td class="diff-line-num new_line old" data-linenumber="2923" 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="LC2898" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//if(pairer -> display_progress)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2899" 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">

2899

</td>

<td class="diff-line-num new_line old" data-linenumber="2923" 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="LC2899" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//  SUBREADprintf("\nThe header was parsed: %d reference sequences were found.\nScanning the input file.\n", pairer -> BAM_n_ref);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2900

</td>

<td class="diff-line-num new_line" data-linenumber="2923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2923

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

<pre style="margin: 0;"> <span id="LC2923" class="line" lang="c">                           <span class="n" style="color: #333;">SAM_pairer_fetch_BAM_block</span><span class="p">(</span><span class="n" style="color: #333;">pairer</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="2901" 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">

2901

</td>

<td class="diff-line-num new_line old" data-linenumber="2924" 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>

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

<pre style="margin: 0;">-<span id="LC2901" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2902" 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">

2902

</td>

<td class="diff-line-num new_line old" data-linenumber="2924" 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="LC2902" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("HEAD_FINISHED, BAD=%d\n", pairer -> is_bad_format);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2903

</td>

<td class="diff-line-num new_line" data-linenumber="2924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2924

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<pre style="margin: 0;"> <span id="LC2924" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2904

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<td class="diff-line-num new_line" data-linenumber="2925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2925

</td>

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

<pre style="margin: 0;"> <span id="LC2925" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2905

</td>

<td class="diff-line-num new_line" data-linenumber="2926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2926

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<pre style="margin: 0;"> <span id="LC2926" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_bad_format</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2935" style="width: 35px; color: rgba(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="2956" style="width: 35px; color: rgba(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">@@ -2935,15 +2956,19 @@ int SAM_pairer_get_next_read_BIN( SAM_pairer_context_t * pairer , SAM_pairer_thr</td>

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<td class="diff-line-num old_line" data-linenumber="2935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2935

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<td class="diff-line-num new_line" data-linenumber="2956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2956

</td>

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

<pre style="margin: 0;"> <span id="LC2956" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2936

</td>

<td class="diff-line-num new_line" data-linenumber="2957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2957

</td>

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

<pre style="margin: 0;"> <span id="LC2957" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2937

</td>

<td class="diff-line-num new_line" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2958

</td>

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

<pre style="margin: 0;"> <span id="LC2958" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2938" style="width: 35px; color: rgba(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="2959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2959

</td>

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

<pre style="margin: 0;">+<span id="LC2959" class="line" lang="c">                   <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("TFMT:RLEN=%d\n", record_len);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2938" style="width: 35px; color: rgba(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="2960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2960

</td>

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

<pre style="margin: 0;">+<span id="LC2960" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2938

</td>

<td class="diff-line-num new_line" data-linenumber="2961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2961

</td>

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

<pre style="margin: 0;"> <span id="LC2961" 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;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_bad_format</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2939

</td>

<td class="diff-line-num new_line" data-linenumber="2962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2962

</td>

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

<pre style="margin: 0;"> <span id="LC2962" class="line" lang="c">                           <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span>  <span class="n" style="color: #333;">seq_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2940

</td>

<td class="diff-line-num new_line" data-linenumber="2963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2963

</td>

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

<pre style="margin: 0;"> <span id="LC2963" class="line" lang="c">                           <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2941

</td>

<td class="diff-line-num new_line" data-linenumber="2964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2964

</td>

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

<pre style="margin: 0;"> <span id="LC2964" class="line" lang="c">                           <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq_len</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_ptr</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">16</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2942

</td>

<td class="diff-line-num new_line" data-linenumber="2965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2965

</td>

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

<pre style="margin: 0;"> <span id="LC2965" class="line" lang="c">                           </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2943

</td>

<td class="diff-line-num new_line" data-linenumber="2966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2966

</td>

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

<pre style="margin: 0;"> <span id="LC2966" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("REDUCE_2: record %u, %u\n", record_len, seq_len);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="2944" 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">

2944

</td>

<td class="diff-line-num new_line old" data-linenumber="2967" 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>

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

<pre style="margin: 0;">-<span id="LC2944" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">record_len</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">record_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">MAX_BIN_RECORD_LENGTH</span><span class="p">,</span><span class="mi" style="color: #099;">60000</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">seq_len</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">long_read_minimum_length</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2945" style="width: 35px; color: rgba(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="2967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2967

</td>

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

<pre style="margin: 0;">+<span id="LC2967" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//                  #warning "=========== CHECK IF '0 && ' IS CORRECT ==========="</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2945" style="width: 35px; color: rgba(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="2968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2968

</td>

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

<pre style="margin: 0;">+<span id="LC2968" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">record_len</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">record_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">MAX_BIN_RECORD_LENGTH</span><span class="p">,</span><span class="mi" style="color: #099;">60000</span><span class="p">))</span><span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">seq_len</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">long_read_minimum_length</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2945

</td>

<td class="diff-line-num new_line" data-linenumber="2969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2969

</td>

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

<pre style="margin: 0;"> <span id="LC2969" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">seq_len</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">long_read_minimum_length</span><span class="p">)</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_single_end_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="2946" 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">

2946

</td>

<td class="diff-line-num new_line old" data-linenumber="2970" 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>

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

<pre style="margin: 0;">-<span id="LC2946" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//  SUBREADprintf("BADFMT: THID=%d; rlen %d; seqlen %d; room %d < %d\n",  thread_context -> thread_id,  record_len, seq_len);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2947" style="width: 35px; color: rgba(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="2970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2970

</td>

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

<pre style="margin: 0;">+<span id="LC2970" class="line" lang="c">                   <span class="c1" style="color: #998; font-style: italic;">//          #warning "BADFORMAT-DEBUG"</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC2971" class="line" lang="c">                   <span class="c1" style="color: #998; font-style: italic;">//          SUBREADprintf("BADFMT: THID=%d; rlen %d; seqlen %d; BIN_PTR=%d\n",  thread_context -> thread_id,  record_len, seq_len, thread_context -> input_buff_BIN_ptr);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2972" class="line" lang="c">                                   <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_bad_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2973" style="width: 35px; color: rgba(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="LC2973" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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2949

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<td class="diff-line-num new_line" data-linenumber="2974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2974

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<pre style="margin: 0;"> <span id="LC2974" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2951" style="width: 35px; color: rgba(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="2976" style="width: 35px; color: rgba(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">@@ -2951,16 +2976,6 @@ int SAM_pairer_get_next_read_BIN( SAM_pairer_context_t * pairer , SAM_pairer_thr</td>

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<pre style="margin: 0;"> <span id="LC2976" class="line" lang="c">                           <span class="p">(</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bin_where</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_ptr</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="2952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2977" style="width: 35px; color: rgba(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="LC2977" class="line" lang="c">                           <span class="p">(</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bin_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2953

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<td class="diff-line-num new_line" data-linenumber="2978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2978

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<pre style="margin: 0;"> <span id="LC2978" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="2979" 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="LC2954" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="2979" 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="LC2955" class="line" lang="c">                                   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Treclen</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;">Tseqlen</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 old old_line" data-linenumber="2956" 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">

2956

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<td class="diff-line-num new_line old" data-linenumber="2979" 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="LC2956" class="line" lang="c">                                   <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Treclen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bin_where</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2957" 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">

2957

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<td class="diff-line-num new_line old" data-linenumber="2979" 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="LC2957" class="line" lang="c">                                   <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Tseqlen</span><span class="p">,</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bin_where</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="2979" 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="LC2958" class="line" lang="c">                                   <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">record_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Treclen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2959" 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="LC2959" class="line" lang="c">                                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">is_bin_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_read_bin</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bin_where</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_used</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_used</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">4</span> <span class="p">,</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">BAM_n_ref</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="2960" 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="LC2960" class="line" lang="c">                                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"TREC TH_%d: reclen=%u, seqlen=%u, IS_BIN=%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">thread_id</span><span class="p">,</span> <span class="n" style="color: #333;">Treclen</span><span class="p">,</span> <span class="n" style="color: #333;">Tseqlen</span><span class="p">,</span> <span class="n" style="color: #333;">is_bin_start</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC2961" class="line" lang="c">                                   <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">is_bin_start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2962" 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">

2962

</td>

<td class="diff-line-num new_line old" data-linenumber="2979" 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="LC2962" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="2963" 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">

2963

</td>

<td class="diff-line-num new_line old" data-linenumber="2979" 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="LC2963" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2964

</td>

<td class="diff-line-num new_line" data-linenumber="2979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2979

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<pre style="margin: 0;"> <span id="LC2979" class="line" lang="c">                           <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">record_len</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2965

</td>

<td class="diff-line-num new_line" data-linenumber="2980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2980

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<pre style="margin: 0;"> <span id="LC2980" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2966

</td>

<td class="diff-line-num new_line" data-linenumber="2981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2981

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<pre style="margin: 0;"> <span id="LC2981" class="line" lang="c">                   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4473" style="width: 35px; color: rgba(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="4488" style="width: 35px; color: rgba(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">@@ -4473,7 +4488,7 @@ int SAM_pairer_find_start(SAM_pairer_context_t * pairer , SAM_pairer_thread_t *</td>

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<td class="diff-line-num old_line" data-linenumber="4473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4473

</td>

<td class="diff-line-num new_line" data-linenumber="4488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4488

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

<pre style="margin: 0;"> <span id="LC4488" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4474

</td>

<td class="diff-line-num new_line" data-linenumber="4489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4489

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<pre style="margin: 0;"> <span id="LC4489" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4475

</td>

<td class="diff-line-num new_line" data-linenumber="4490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4490

</td>

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

<pre style="margin: 0;"> <span id="LC4490" class="line" lang="c">   <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start_pos</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4476" 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">

4476

</td>

<td class="diff-line-num new_line old" data-linenumber="4491" 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>

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

<pre style="margin: 0;">-<span id="LC4476" class="line" lang="c"><span class="idiff left">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//</span>SUBREADprintf("ABBO TH %d : FOUND START AT %d in %d\n", thread_context -> thread_id , start_pos, thread_context -> input_buff_BIN_used);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4477" style="width: 35px; color: rgba(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="4491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4491

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

<pre style="margin: 0;">+<span id="LC4491" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//      </span>SUBREADprintf("ABBO TH %d : FOUND START AT %d in %d\n", thread_context -> thread_id , start_pos, thread_context -> input_buff_BIN_used);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4477

</td>

<td class="diff-line-num new_line" data-linenumber="4492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4492

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

<pre style="margin: 0;"> <span id="LC4492" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">MAX_BIN_RECORD_LENGTH</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">input_buff_BIN_used</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4478

</td>

<td class="diff-line-num new_line" data-linenumber="4493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4493

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

<pre style="margin: 0;"> <span id="LC4493" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4479

</td>

<td class="diff-line-num new_line" data-linenumber="4494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4494

</td>

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

<pre style="margin: 0;"> <span id="LC4494" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4700" style="width: 35px; color: rgba(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="4715" style="width: 35px; color: rgba(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">@@ -4700,70 +4715,81 @@ int fix_load_next_block(FILE * in, char * binbuf, z_stream * strm){</td>

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<td class="diff-line-num old_line" data-linenumber="4700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4700

</td>

<td class="diff-line-num new_line" data-linenumber="4715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4715

</td>

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

<pre style="margin: 0;"> <span id="LC4715" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4701

</td>

<td class="diff-line-num new_line" data-linenumber="4716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4716

</td>

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

<pre style="margin: 0;"> <span id="LC4716" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4702

</td>

<td class="diff-line-num new_line" data-linenumber="4717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4717

</td>

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

<pre style="margin: 0;"> <span id="LC4717" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span>  <span class="nf" style="color: #900; font-weight: 600;">fix_write_block</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bin</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">binlen</span><span class="p">,</span> <span class="n" style="color: #333;">z_stream</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">strm</span><span class="p">){</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4703" 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">

4703

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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="LC4703" 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;">bam_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="mi" style="color: #099;">70000</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4704" 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">

4704

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC4704" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="n" style="color: #333;">bam_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4705" 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">

4705

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC4705" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4706" 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">

4706

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4706" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">binlen</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4707" 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">

4707

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC4707" class="line" lang="c">           <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">binlen</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4708" 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">

4708

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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="LC4708" class="line" lang="c">           <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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;">bin</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4709" 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">

4709

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4709" class="line" lang="c">           <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">70000</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4710" 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">

4710

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4710" class="line" lang="c">           <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">next_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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;">bam_buf</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4711" 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">

4711

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4711" class="line" lang="c">           <span class="n" style="color: #333;">deflate</span><span class="p">(</span><span class="n" style="color: #333;">strm</span> <span class="p">,</span> <span class="n" style="color: #333;">Z_FINISH</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4712" 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">

4712

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4712" class="line" lang="c">           <span class="n" style="color: #333;">bam_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">70000</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">avail_out</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4713" 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">

4713

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4713" class="line" lang="c">           <span class="n" style="color: #333;">deflateReset</span><span class="p">(</span><span class="n" style="color: #333;">strm</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4714" 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">

4714

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4714" class="line" lang="c">   <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4715" 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">

4715

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4715" class="line" lang="c">           <span class="n" style="color: #333;">z_stream</span> <span class="n" style="color: #333;">nstrm</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4716" 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">

4716

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4716" class="line" lang="c">           <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">zalloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4717" 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">

4717

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4717" class="line" lang="c">           <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">zfree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4718" 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">

4718

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4718" class="line" lang="c">           <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">opaque</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4719" 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">

4719

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4719" class="line" lang="c">           <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4720" 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">

4720

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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="LC4720" class="line" lang="c">           <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4721" 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">

4721

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4721" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4722" 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">

4722

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4722" class="line" lang="c">           <span class="n" style="color: #333;">deflateInit2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nstrm</span><span class="p">,</span> <span class="n" style="color: #333;">SAMBAM_COMPRESS_LEVEL</span><span class="p">,</span> <span class="n" style="color: #333;">Z_DEFLATED</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4723" 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">

4723

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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>

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

<pre style="margin: 0;">-<span id="LC4723" class="line" lang="c">                   <span class="n" style="color: #333;">PAIRER_GZIP_WINDOW_BITS</span><span class="p">,</span> <span class="n" style="color: #333;">PAIRER_DEFAULT_MEM_LEVEL</span><span class="p">,</span> <span class="n" style="color: #333;">Z_DEFAULT_STRATEGY</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4724" style="width: 35px; color: rgba(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="4718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4718

</td>

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

<pre style="margin: 0;">+<span id="LC4718" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">is_end_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">binlen</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;">written</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4724" style="width: 35px; color: rgba(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="4719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4719

</td>

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

<pre style="margin: 0;">+<span id="LC4719" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("FIX_WRTR : %d\n", binlen);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4724

</td>

<td class="diff-line-num new_line" data-linenumber="4720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4720

</td>

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

<pre style="margin: 0;"> <span id="LC4720" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4725" 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">

4725

</td>

<td class="diff-line-num new_line old" data-linenumber="4721" 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>

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

<pre style="margin: 0;">-<span id="LC4725" class="line" lang="c">           <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4726" 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">

4726

</td>

<td class="diff-line-num new_line old" data-linenumber="4721" 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>

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

<pre style="margin: 0;">-<span id="LC4726" class="line" lang="c">           <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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;">bin</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4727" 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">

4727

</td>

<td class="diff-line-num new_line old" data-linenumber="4721" 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>

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

<pre style="margin: 0;">-<span id="LC4727" class="line" lang="c">           <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">70000</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4728" 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">

4728

</td>

<td class="diff-line-num new_line old" data-linenumber="4721" 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>

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

<pre style="margin: 0;">-<span id="LC4728" class="line" lang="c">           <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">next_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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;">bam_buf</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4729" 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">

4729

</td>

<td class="diff-line-num new_line old" data-linenumber="4721" 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>

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

<pre style="margin: 0;">-<span id="LC4729" class="line" lang="c">           <span class="n" style="color: #333;">deflate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nstrm</span><span class="p">,</span> <span class="n" style="color: #333;">Z_FINISH</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4730" 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">

4730

</td>

<td class="diff-line-num new_line old" data-linenumber="4721" 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>

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

<pre style="margin: 0;">-<span id="LC4730" class="line" lang="c">           <span class="n" style="color: #333;">bam_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">70000</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">avail_out</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4731" 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">

4731

</td>

<td class="diff-line-num new_line old" data-linenumber="4721" 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>

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

<pre style="margin: 0;">-<span id="LC4731" class="line" lang="c">           <span class="n" style="color: #333;">deflateEnd</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nstrm</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4732" 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">

4732

</td>

<td class="diff-line-num new_line old" data-linenumber="4721" 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>

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

<pre style="margin: 0;">-<span id="LC4732" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4733" style="width: 35px; color: rgba(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="4721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4721

</td>

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

<pre style="margin: 0;">+<span id="LC4721" class="line" lang="c">   <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4733" style="width: 35px; color: rgba(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="4722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4722

</td>

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

<pre style="margin: 0;">+<span id="LC4722" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">binlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">written</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">is_end_mode</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4733

</td>

<td class="diff-line-num new_line" data-linenumber="4723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4723

</td>

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

<pre style="margin: 0;"> <span id="LC4723" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4734" 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">

4734

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4734" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("FIX_COMPR: %d -> %d  RET=%d\n", binlen , bam_len, retbam);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4735" 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">

4735

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4735" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4736" 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">

4736

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4736" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">crc0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crc32</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4737" 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">

4737

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4737" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">crc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crc32</span><span class="p">(</span><span class="n" style="color: #333;">crc0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">bin</span> <span class="p">,</span> <span class="n" style="color: #333;">binlen</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4738" 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">

4738

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4738" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4739" 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">

4739

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4739" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">31</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4740" 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">

4740

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4740" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">139</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4741" 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">

4741

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4741" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4742" 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">

4742

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4742" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4743" 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">

4743

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4743" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4744" 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">

4744

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4744" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4745" 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">

4745

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4745" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4746" 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">

4746

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4746" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4747" 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">

4747

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4747" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4748" 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">

4748

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4748" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//XFL</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4749" 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">

4749

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4749" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mh" style="color: #099;">0xff</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//OS</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4750" 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">

4750

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4750" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4751" 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">

4751

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4751" class="line" lang="c">   <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4752" 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">

4752

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4752" class="line" lang="c">   <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4753" 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">

4753

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4753" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span> <span class="mi" style="color: #099;">66</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4754" 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">

4754

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4754" class="line" lang="c">   <span class="n" style="color: #333;">fputc</span><span class="p">(</span> <span class="mi" style="color: #099;">67</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4755" 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">

4755

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4755" class="line" lang="c">   <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4756" 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">

4756

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4756" class="line" lang="c">   <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4757" 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">

4757

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4757" class="line" lang="c">   <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">19</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4758" 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">

4758

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4758" class="line" lang="c">   <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4759" 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">

4759

</td>

<td class="diff-line-num new_line old" data-linenumber="4724" 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>

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

<pre style="margin: 0;">-<span id="LC4759" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">write_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="n" style="color: #333;">bam_buf</span> <span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">bam_len</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4760" style="width: 35px; color: rgba(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="4724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4724

</td>

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

<pre style="margin: 0;">+<span id="LC4724" 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;">bam_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="mi" style="color: #099;">70000</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4760" style="width: 35px; color: rgba(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="4725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4725

</td>

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

<pre style="margin: 0;">+<span id="LC4725" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="n" style="color: #333;">bam_len</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;">old_in</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;">this_sec_len</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;">old_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">written</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4760

</td>

<td class="diff-line-num new_line" data-linenumber="4726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4726

</td>

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

<pre style="margin: 0;"> <span id="LC4726" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4761" 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">

4761

</td>

<td class="diff-line-num new_line old" data-linenumber="4727" 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>

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

<pre style="margin: 0;">-<span id="LC4761" class="line" lang="c">   <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">crc</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4762" 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">

4762

</td>

<td class="diff-line-num new_line old" data-linenumber="4727" 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>

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

<pre style="margin: 0;">-<span id="LC4762" class="line" lang="c">   <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">binlen</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4763" 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">

4763

</td>

<td class="diff-line-num new_line old" data-linenumber="4727" 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>

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

<pre style="margin: 0;">-<span id="LC4763" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4764" 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">

4764

</td>

<td class="diff-line-num new_line old" data-linenumber="4727" 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>

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

<pre style="margin: 0;">-<span id="LC4764" class="line" lang="c">   <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">bam_buf</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4765" 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">

4765

</td>

<td class="diff-line-num new_line old" data-linenumber="4727" 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>

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

<pre style="margin: 0;">-<span id="LC4765" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4766" 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">

4766

</td>

<td class="diff-line-num new_line old" data-linenumber="4727" 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>

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

<pre style="margin: 0;">-<span id="LC4766" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">write_len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bam_len</span><span class="p">)</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4727

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

<pre style="margin: 0;">+<span id="LC4727" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">binlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4728

</td>

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

<pre style="margin: 0;">+<span id="LC4728" class="line" lang="c">                   <span class="n" style="color: #333;">old_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">binlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">written</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4729

</td>

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

<pre style="margin: 0;">+<span id="LC4729" class="line" lang="c">                   <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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;">bin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">written</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4730

</td>

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

<pre style="margin: 0;">+<span id="LC4730" class="line" lang="c">                   <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">70000</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4731

</td>

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

<pre style="margin: 0;">+<span id="LC4731" class="line" lang="c">                   <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">next_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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;">bam_buf</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4732

</td>

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

<pre style="margin: 0;">+<span id="LC4732" class="line" lang="c">                   <span class="n" style="color: #333;">deflate</span><span class="p">(</span><span class="n" style="color: #333;">strm</span> <span class="p">,</span> <span class="n" style="color: #333;">Z_FINISH</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4733

</td>

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

<pre style="margin: 0;">+<span id="LC4733" class="line" lang="c">                   <span class="n" style="color: #333;">bam_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">70000</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">avail_out</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4734

</td>

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

<pre style="margin: 0;">+<span id="LC4734" class="line" lang="c">                   <span class="n" style="color: #333;">this_sec_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_in</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">strm</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">avail_in</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4735

</td>

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

<pre style="margin: 0;">+<span id="LC4735" class="line" lang="c">                   <span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">this_sec_len</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4736

</td>

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

<pre style="margin: 0;">+<span id="LC4736" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4737

</td>

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

<pre style="margin: 0;">+<span id="LC4737" class="line" lang="c">                   <span class="n" style="color: #333;">deflateReset</span><span class="p">(</span><span class="n" style="color: #333;">strm</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4738

</td>

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

<pre style="margin: 0;">+<span id="LC4738" class="line" lang="c">           <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4739

</td>

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

<pre style="margin: 0;">+<span id="LC4739" class="line" lang="c">                   <span class="n" style="color: #333;">z_stream</span> <span class="n" style="color: #333;">nstrm</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4740

</td>

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

<pre style="margin: 0;">+<span id="LC4740" class="line" lang="c">                   <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">zalloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4741

</td>

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

<pre style="margin: 0;">+<span id="LC4741" class="line" lang="c">                   <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">zfree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

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</td>

<td class="diff-line-num new new_line" data-linenumber="4742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4742

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<pre style="margin: 0;">+<span id="LC4742" class="line" lang="c">                   <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">opaque</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4743

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<pre style="margin: 0;">+<span id="LC4743" class="line" lang="c">                   <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4744

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<pre style="margin: 0;">+<span id="LC4744" class="line" lang="c">                   <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4745

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<pre style="margin: 0;">+<span id="LC4745" class="line" lang="c">           </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4746

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<pre style="margin: 0;">+<span id="LC4746" class="line" lang="c">                   <span class="n" style="color: #333;">deflateInit2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nstrm</span><span class="p">,</span> <span class="n" style="color: #333;">SAMBAM_COMPRESS_LEVEL</span><span class="p">,</span> <span class="n" style="color: #333;">Z_DEFLATED</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4747

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<pre style="margin: 0;">+<span id="LC4747" class="line" lang="c">                           <span class="n" style="color: #333;">PAIRER_GZIP_WINDOW_BITS</span><span class="p">,</span> <span class="n" style="color: #333;">PAIRER_DEFAULT_MEM_LEVEL</span><span class="p">,</span> <span class="n" style="color: #333;">Z_DEFAULT_STRATEGY</span><span class="p">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4748

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<pre style="margin: 0;">+<span id="LC4748" class="line" lang="c">   </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4749

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<pre style="margin: 0;">+<span id="LC4749" class="line" lang="c">                   <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4750

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<pre style="margin: 0;">+<span id="LC4750" class="line" lang="c">                   <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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;">bin</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4751

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<pre style="margin: 0;">+<span id="LC4751" class="line" lang="c">                   <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">70000</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4752

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<pre style="margin: 0;">+<span id="LC4752" class="line" lang="c">                   <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">next_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="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;">bam_buf</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4753

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<pre style="margin: 0;">+<span id="LC4753" class="line" lang="c">                   <span class="n" style="color: #333;">deflate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nstrm</span><span class="p">,</span> <span class="n" style="color: #333;">Z_FINISH</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4754

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<pre style="margin: 0;">+<span id="LC4754" class="line" lang="c">                   <span class="n" style="color: #333;">bam_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">70000</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nstrm</span><span class="p">.</span><span class="n" style="color: #333;">avail_out</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4755

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<pre style="margin: 0;">+<span id="LC4755" class="line" lang="c">                   <span class="n" style="color: #333;">deflateEnd</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nstrm</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4756

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<pre style="margin: 0;">+<span id="LC4756" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4757

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<pre style="margin: 0;">+<span id="LC4757" class="line" lang="c">   </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4758

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<pre style="margin: 0;">+<span id="LC4758" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("FIX_COMPR: %d -> %d  RET=%d\n", binlen , bam_len, retbam);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4759

</td>

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

<pre style="margin: 0;">+<span id="LC4759" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4760

</td>

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

<pre style="margin: 0;">+<span id="LC4760" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">crc0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crc32</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4761

</td>

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

<pre style="margin: 0;">+<span id="LC4761" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">crc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crc32</span><span class="p">(</span><span class="n" style="color: #333;">crc0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">old_start</span><span class="p">,</span> <span class="n" style="color: #333;">this_sec_len</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4762

</td>

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

<pre style="margin: 0;">+<span id="LC4762" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4763

</td>

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

<pre style="margin: 0;">+<span id="LC4763" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">31</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4764

</td>

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

<pre style="margin: 0;">+<span id="LC4764" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">139</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4765

</td>

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

<pre style="margin: 0;">+<span id="LC4765" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4766

</td>

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

<pre style="margin: 0;">+<span id="LC4766" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4767

</td>

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

<pre style="margin: 0;">+<span id="LC4767" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4768

</td>

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

<pre style="margin: 0;">+<span id="LC4768" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4769

</td>

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

<pre style="margin: 0;">+<span id="LC4769" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4770

</td>

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

<pre style="margin: 0;">+<span id="LC4770" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4771

</td>

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

<pre style="margin: 0;">+<span id="LC4771" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4772

</td>

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

<pre style="margin: 0;">+<span id="LC4772" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//XFL</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4773

</td>

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

<pre style="margin: 0;">+<span id="LC4773" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="mh" style="color: #099;">0xff</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//OS</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4774

</td>

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

<pre style="margin: 0;">+<span id="LC4774" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4775

</td>

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

<pre style="margin: 0;">+<span id="LC4775" class="line" lang="c">           <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4776

</td>

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

<pre style="margin: 0;">+<span id="LC4776" class="line" lang="c">           <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4777

</td>

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

<pre style="margin: 0;">+<span id="LC4777" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span> <span class="mi" style="color: #099;">66</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4778

</td>

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

<pre style="margin: 0;">+<span id="LC4778" class="line" lang="c">           <span class="n" style="color: #333;">fputc</span><span class="p">(</span> <span class="mi" style="color: #099;">67</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4779

</td>

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

<pre style="margin: 0;">+<span id="LC4779" class="line" lang="c">           <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4780

</td>

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

<pre style="margin: 0;">+<span id="LC4780" class="line" lang="c">           <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4781

</td>

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

<pre style="margin: 0;">+<span id="LC4781" class="line" lang="c">           <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">19</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4782

</td>

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

<pre style="margin: 0;">+<span id="LC4782" class="line" lang="c">           <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4783

</td>

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

<pre style="margin: 0;">+<span id="LC4783" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">write_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="n" style="color: #333;">bam_buf</span> <span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">bam_len</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4784

</td>

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

<pre style="margin: 0;">+<span id="LC4784" class="line" lang="c">           </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4785

</td>

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

<pre style="margin: 0;">+<span id="LC4785" class="line" lang="c">           <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">crc</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4786

</td>

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

<pre style="margin: 0;">+<span id="LC4786" class="line" lang="c">           <span class="n" style="color: #333;">fwrite</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">binlen</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4787

</td>

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

<pre style="margin: 0;">+<span id="LC4787" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4788

</td>

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

<pre style="margin: 0;">+<span id="LC4788" class="line" lang="c">           <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">bam_buf</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4789

</td>

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

<pre style="margin: 0;">+<span id="LC4789" class="line" lang="c">   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4790

</td>

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

<pre style="margin: 0;">+<span id="LC4790" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">write_len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bam_len</span><span class="p">)</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4791

</td>

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

<pre style="margin: 0;">+<span id="LC4791" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">binlen</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="4767" style="width: 35px; color: rgba(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="4792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4792

</td>

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

<pre style="margin: 0;">+<span id="LC4792" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4767

</td>

<td class="diff-line-num new_line" data-linenumber="4793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4793

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

<pre style="margin: 0;"> <span id="LC4793" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4768

</td>

<td class="diff-line-num new_line" data-linenumber="4794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4794

</td>

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

<pre style="margin: 0;"> <span id="LC4794" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4769

</td>

<td class="diff-line-num new_line" data-linenumber="4795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4795

</td>

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

<pre style="margin: 0;"> <span id="LC4795" class="line" lang="c"></span>

</pre>

</td>

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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="4775" style="width: 35px; color: rgba(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="4801" style="width: 35px; color: rgba(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">@@ -4775,7 +4801,7 @@ int  fix_write_block(FILE * out, char * bin, int binlen, z_stream * strm){</td>

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

<td class="diff-line-num old_line" data-linenumber="4775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4775

</td>

<td class="diff-line-num new_line" data-linenumber="4801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4801

</td>

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

<pre style="margin: 0;"> <span id="LC4801" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4776

</td>

<td class="diff-line-num new_line" data-linenumber="4802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4802

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<pre style="margin: 0;"> <span id="LC4802" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FIX_FLASH_OUT { if(out_bin_ptr > 0)disk_is_full |= fix_write_block(new_fp, out_bin, out_bin_ptr, &out_strm); out_bin_ptr = 0; }</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4777

</td>

<td class="diff-line-num new_line" data-linenumber="4803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4803

</td>

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

<pre style="margin: 0;"> <span id="LC4803" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4778" 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">

4778

</td>

<td class="diff-line-num new_line old" data-linenumber="4804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC4778" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FIX_APPEND_OUT(p, c) { if(out_bin_ptr > 6000<span class="idiff left right">0</span>){FIX_FLASH_OUT} ;  memcpy(out_bin + out_bin_ptr, p, c); out_bin_ptr +=c ; }</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="4779" style="width: 35px; color: rgba(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="4804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4804

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

<pre style="margin: 0;">+<span id="LC4804" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FIX_APPEND_OUT(p, c) { if(out_bin_ptr > 6000<span class="idiff left right">2</span>){FIX_FLASH_OUT} ;  memcpy(out_bin + out_bin_ptr, p, c); out_bin_ptr +=c ; }</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4779

</td>

<td class="diff-line-num new_line" data-linenumber="4805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4805

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<pre style="margin: 0;"> <span id="LC4805" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FIX_APPEND_READ(p, c){ memcpy(out_bin + out_bin_ptr, p, c); out_bin_ptr +=c ;  }</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4780

</td>

<td class="diff-line-num new_line" data-linenumber="4806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4806

</td>

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

<pre style="margin: 0;"> <span id="LC4806" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4781

</td>

<td class="diff-line-num new_line" data-linenumber="4807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4807

</td>

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

<pre style="margin: 0;"> <span id="LC4807" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">SAM_pairer_fix_format</span><span class="p">(</span><span class="n" style="color: #333;">SAM_pairer_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pairer</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4786" style="width: 35px; color: rgba(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="4812" style="width: 35px; color: rgba(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">@@ -4786,8 +4812,8 @@ int SAM_pairer_fix_format(SAM_pairer_context_t * pairer){</td>

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<td class="diff-line-num old_line" data-linenumber="4786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4786

</td>

<td class="diff-line-num new_line" data-linenumber="4812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4812

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<pre style="margin: 0;"> <span id="LC4812" class="line" lang="c">   <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tmpfname</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.fixbam"</span><span class="p">,</span> <span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">tmp_file_prefix</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4787

</td>

<td class="diff-line-num new_line" data-linenumber="4813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4813

</td>

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

<pre style="margin: 0;"> <span id="LC4813" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4788

</td>

<td class="diff-line-num new_line" data-linenumber="4814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4814

</td>

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

<pre style="margin: 0;"> <span id="LC4814" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f_subr_open</span><span class="p">(</span><span class="n" style="color: #333;">tmpfname</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4789" 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">

4789

</td>

<td class="diff-line-num new_line old" data-linenumber="4815" 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="LC4789" 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;">in_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="mi" style="color: #099;">1<span class="idiff left right">4000</span>0</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="4790" 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">

4790

</td>

<td class="diff-line-num new_line old" data-linenumber="4815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC4790" 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;">out_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">70000</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4791" style="width: 35px; color: rgba(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="4815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4815

</td>

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<pre style="margin: 0;">+<span id="LC4815" 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;">in_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="mi" style="color: #099;">1<span class="idiff left">024</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff right">7</span>0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4791" style="width: 35px; color: rgba(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="4816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4816

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<pre style="margin: 0;">+<span id="LC4816" 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;">out_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">20</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">1024</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff right">1024</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4791

</td>

<td class="diff-line-num new_line" data-linenumber="4817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4817

</td>

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

<pre style="margin: 0;"> <span id="LC4817" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4792

</td>

<td class="diff-line-num new_line" data-linenumber="4818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4818

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<pre style="margin: 0;"> <span id="LC4818" class="line" lang="c">   <span class="n" style="color: #333;">z_stream</span> <span class="n" style="color: #333;">in_strm</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4793

</td>

<td class="diff-line-num new_line" data-linenumber="4819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4819

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<pre style="margin: 0;"> <span id="LC4819" class="line" lang="c">   <span class="n" style="color: #333;">z_stream</span> <span class="n" style="color: #333;">out_strm</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4849" style="width: 35px; color: rgba(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="4875" style="width: 35px; color: rgba(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">@@ -4849,7 +4875,7 @@ int SAM_pairer_fix_format(SAM_pairer_context_t * pairer){</td>

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<td class="diff-line-num old_line" data-linenumber="4849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4849

</td>

<td class="diff-line-num new_line" data-linenumber="4875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4875

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<pre style="margin: 0;"> <span id="LC4875" class="line" lang="c">           <span class="n" style="color: #333;">content_size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">nch</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4850

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<td class="diff-line-num new_line" data-linenumber="4876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4876

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<pre style="margin: 0;"> <span id="LC4876" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4851

</td>

<td class="diff-line-num new_line" data-linenumber="4877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4877

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<pre style="margin: 0;"> <span id="LC4877" class="line" lang="c">   <span class="n" style="color: #333;">FIX_APPEND_OUT</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">content_size</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4852" 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">

4852

</td>

<td class="diff-line-num new_line old" data-linenumber="4878" 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="LC4852" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("FIX: CHROLEN=%d\n", content_size);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4853" style="width: 35px; color: rgba(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="4878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4878

</td>

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

<pre style="margin: 0;">+<span id="LC4878" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("<span class="idiff left right">LONG</span>FIX: CHROLEN=%d\n", content_size);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4853

</td>

<td class="diff-line-num new_line" data-linenumber="4879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4879

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<pre style="margin: 0;"> <span id="LC4879" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">content_count</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;">content_count</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">content_size</span><span class="p">;</span> <span class="n" style="color: #333;">content_count</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4854

</td>

<td class="diff-line-num new_line" data-linenumber="4880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4880

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<pre style="margin: 0;"> <span id="LC4880" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">namelen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4855

</td>

<td class="diff-line-num new_line" data-linenumber="4881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4881

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<pre style="margin: 0;"> <span id="LC4881" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4864" style="width: 35px; color: rgba(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="4890" style="width: 35px; color: rgba(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">@@ -4864,7 +4890,7 @@ int SAM_pairer_fix_format(SAM_pairer_context_t * pairer){</td>

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<td class="diff-line-num old_line" data-linenumber="4864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4864

</td>

<td class="diff-line-num new_line" data-linenumber="4890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4890

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

<pre style="margin: 0;"> <span id="LC4890" class="line" lang="c">                   <span class="n" style="color: #333;">FIX_APPEND_READ</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nch</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4865

</td>

<td class="diff-line-num new_line" data-linenumber="4891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4891

</td>

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

<pre style="margin: 0;"> <span id="LC4891" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4866

</td>

<td class="diff-line-num new_line" data-linenumber="4892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4892

</td>

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

<pre style="margin: 0;"> <span id="LC4892" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4867" 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">

4867

</td>

<td class="diff-line-num new_line old" data-linenumber="4893" 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>

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

<pre style="margin: 0;">-<span id="LC4867" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">out_bin_ptr</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">6000<span class="idiff left right">0</span></span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4868" style="width: 35px; color: rgba(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="4893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4893

</td>

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

<pre style="margin: 0;">+<span id="LC4893" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">out_bin_ptr</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">6000<span class="idiff left right">3</span></span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4868

</td>

<td class="diff-line-num new_line" data-linenumber="4894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4894

</td>

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

<pre style="margin: 0;"> <span id="LC4894" class="line" lang="c">                   <span class="n" style="color: #333;">FIX_FLASH_OUT</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4869

</td>

<td class="diff-line-num new_line" data-linenumber="4895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4895

</td>

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

<pre style="margin: 0;"> <span id="LC4895" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4870

</td>

<td class="diff-line-num new_line" data-linenumber="4896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4896

</td>

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

<pre style="margin: 0;"> <span id="LC4896" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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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="4891" style="width: 35px; color: rgba(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="4917" style="width: 35px; color: rgba(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">@@ -4891,9 +4917,6 @@ int SAM_pairer_fix_format(SAM_pairer_context_t * pairer){</td>

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<td class="diff-line-num old_line" data-linenumber="4891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4891

</td>

<td class="diff-line-num new_line" data-linenumber="4917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4917

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<pre style="margin: 0;"> <span id="LC4917" class="line" lang="c">                   <span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">nch</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4892

</td>

<td class="diff-line-num new_line" data-linenumber="4918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4918

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

<pre style="margin: 0;"> <span id="LC4918" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4893

</td>

<td class="diff-line-num new_line" data-linenumber="4919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4919

</td>

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

<pre style="margin: 0;"> <span id="LC4919" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4894" 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">

4894

</td>

<td class="diff-line-num new_line old" data-linenumber="4920" 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>

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

<pre style="margin: 0;">-<span id="LC4894" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_bin_ptr</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">60000</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">tiny_mode</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4895" 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">

4895

</td>

<td class="diff-line-num new_line old" data-linenumber="4920" 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>

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

<pre style="margin: 0;">-<span id="LC4895" class="line" lang="c">                   <span class="n" style="color: #333;">FIX_FLASH_OUT</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4896" 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">

4896

</td>

<td class="diff-line-num new_line old" data-linenumber="4920" 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>

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

<pre style="margin: 0;">-<span id="LC4896" class="line" lang="c"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="4897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4897

</td>

<td class="diff-line-num new_line" data-linenumber="4920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4920

</td>

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

<pre style="margin: 0;"> <span id="LC4920" class="line" lang="c">           <span class="n" style="color: #333;">FIX_APPEND_READ</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">block_size</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4898

</td>

<td class="diff-line-num new_line" data-linenumber="4921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4921

</td>

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

<pre style="margin: 0;"> <span id="LC4921" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4899

</td>

<td class="diff-line-num new_line" data-linenumber="4922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4922

</td>

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

<pre style="margin: 0;"> <span id="LC4922" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pairer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">tiny_mode</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4927" style="width: 35px; color: rgba(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="4950" style="width: 35px; color: rgba(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">@@ -4927,7 +4950,9 @@ int SAM_pairer_fix_format(SAM_pairer_context_t * pairer){</td>

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<td class="diff-line-num old_line" data-linenumber="4927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4927

</td>

<td class="diff-line-num new_line" data-linenumber="4950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4950

</td>

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

<pre style="margin: 0;"> <span id="LC4950" class="line" lang="c">                                   <span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="4928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4928

</td>

<td class="diff-line-num new_line" data-linenumber="4951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4951

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4951" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4929

</td>

<td class="diff-line-num 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">

4952

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4952" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4930" 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">

4930

</td>

<td class="diff-line-num new_line old" data-linenumber="4953" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4930" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">60000</span> <span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4931" style="width: 35px; color: rgba(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="4953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4953

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4953" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4931" style="width: 35px; color: rgba(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="4954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4954

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4954" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//                  #warning "================ THIS BLOCK WAS DISABLED ON 03OCT2019; MAKE SURE IT WORKS ON LONG READS/LONG READ RECORDS =============="</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4931" style="width: 35px; color: rgba(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="4955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4955

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4955" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">60000</span> <span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4931

</td>

<td class="diff-line-num new_line" data-linenumber="4956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4956

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4956" class="line" lang="c">                                   <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4932

</td>

<td class="diff-line-num new_line" data-linenumber="4957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4957

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4957" class="line" lang="c">                                   <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"   ERROR: Alignment record is too long."</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4933

</td>

<td class="diff-line-num new_line" data-linenumber="4958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4958

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4958" class="line" lang="c">                                   <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"          Please use the long read mode."</span><span class="p">);</span></span>

</pre>

</td>

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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="5054" style="width: 35px; color: rgba(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="5079" style="width: 35px; color: rgba(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">@@ -5054,10 +5079,9 @@ int SAM_pairer_fix_format(SAM_pairer_context_t * pairer){</td>

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<td class="diff-line-num old_line" data-linenumber="5054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5054

</td>

<td class="diff-line-num new_line" data-linenumber="5079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5079

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5079" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5055

</td>

<td class="diff-line-num new_line" data-linenumber="5080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5080

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5080" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5056

</td>

<td class="diff-line-num new_line" data-linenumber="5081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5081

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5081" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="5057" 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">

5057

</td>

<td class="diff-line-num new_line old" data-linenumber="5082" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5057" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;">//#warning "========= COMMENT NEXT ============="</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="5058" 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">

5058

</td>

<td class="diff-line-num new_line old" data-linenumber="5082" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5058" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("OUTBIN_PTR=%d\n", out_bin_ptr);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5059

</td>

<td class="diff-line-num new_line" data-linenumber="5082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5082

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5082" class="line" lang="c">           <span class="n" style="color: #333;">reads</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5060

</td>

<td class="diff-line-num new_line" data-linenumber="5083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5083

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5083" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">out_bin_ptr</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">60000</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="5061" style="width: 35px; color: rgba(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="5084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5084

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5084" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//          SUBREADprintf("WRIR3: TINY=%d\n", pairer -> tiny_mode);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5061

</td>

<td class="diff-line-num new_line" data-linenumber="5085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5085

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5085" class="line" lang="c">                   <span class="n" style="color: #333;">FIX_FLASH_OUT</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5062

</td>

<td class="diff-line-num new_line" data-linenumber="5086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5086

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5086" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5063

</td>

<td class="diff-line-num new_line" data-linenumber="5087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5087

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5087" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="6907133cceb8c785482dac4a3125dbff95a3d8e2">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#6907133cceb8c785482dac4a3125dbff95a3d8e2"><strong>src/input-files.h</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,6 +102,7 @@ typedef struct {</td>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">input_buff_BIN</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">input_buff_BIN_used</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">input_buff_BIN_ptr</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">input_buff_BIN_capacity</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">orphant_block_no</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">need_find_start</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c">    <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">orphant_space</span><span class="p">;</span></span>

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</li>

<li id="76cc7b82fd823387133c6778766e61c15828100c">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#76cc7b82fd823387133c6778766e61c15828100c"><strong>src/makefile.version</strong></a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">SUBREAD_VERSION_BASE</span><span class="o" style="font-weight: 600;">=</span>2.0.<span class="idiff left right">0</span></span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">SUBREAD_VERSION_BASE</span><span class="o" style="font-weight: 600;">=</span>2.0.<span class="idiff left right">1</span></span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nv" style="color: #008080;">SUBREAD_VERSION_DATE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(SUBREAD_VERSION_BASE)</span>-<span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">date</span> +<span class="s2" style="color: #d14;">"%d%b%Y"</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="nv" style="color: #008080;">SUBREAD_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(SUBREAD_VERSION_DATE)</span><span class="s2" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nv" style="color: #008080;">SUBREAD_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(SUBREAD_VERSION_BASE)</span><span class="s2" style="color: #d14;">"</span></span>

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<li id="2ec8748eb117e101c7a40d2a3e3c5d8cf22f9dd9">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#2ec8748eb117e101c7a40d2a3e3c5d8cf22f9dd9"><strong>src/readSummary.c</strong></a>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FC_FLIST_SPLITOR "\026"</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;"><span class="idiff left">gene_name</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">FEATURE_NAME_LENGTH</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">gene_name</span></span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos_first_base</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(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="LC69" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos_last_base</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 class="n" style="color: #333;">fc_junction_gene_t</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -97,7 +97,7 @@ typedef struct {</td>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">fc_junction_info_t</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(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="LC98" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">feature_name_pos</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c">    <span class="n" style="color: #333;"><span class="idiff left right">srInt_64</span></span> <span class="n" style="color: #333;">feature_name_pos</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(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="LC103" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sorted_order</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -280,8 +280,8 @@ typedef struct {</td>

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<pre style="margin: 0;"> <span id="LC280" 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;">debug_command</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC281" 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;">unistr_buffer_space</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c">    <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">max_BAM_header_size</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">unistr_buffer_size</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">unistr_buffer_used</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="c">    <span class="n" style="color: #333;"><span class="idiff left right">srInt_64</span></span> <span class="n" style="color: #333;">unistr_buffer_size</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="c">    <span class="n" style="color: #333;"><span class="idiff left right">srInt_64</span></span> <span class="n" style="color: #333;">unistr_buffer_used</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="285" style="width: 35px; color: rgba(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="LC285" class="line" lang="c">    <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scRNA_sample_sheet_table</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="286" style="width: 35px; color: rgba(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="LC286" class="line" lang="c">    <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scRNA_sample_barcode_list</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="287" style="width: 35px; color: rgba(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="LC287" class="line" lang="c">    <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scRNA_cell_barcodes_array</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="323" style="width: 35px; color: rgba(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="323" style="width: 35px; color: rgba(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">@@ -323,7 +323,7 @@ typedef struct {</td>

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<pre style="margin: 0;"> <span id="LC323" 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;">exontable_chr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="324" style="width: 35px; color: rgba(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="LC324" class="line" lang="c">    <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">exontable_start</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="325" style="width: 35px; color: rgba(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="LC325" class="line" lang="c">    <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">exontable_stop</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="326" 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="LC326" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">feature_name_column</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span>00</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="327" style="width: 35px; color: rgba(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="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">feature_name_column</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">20</span>00</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

327

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<td class="diff-line-num new_line" data-linenumber="327" style="width: 35px; color: rgba(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="LC327" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gene_id_column</span><span class="p">[</span><span class="mi" style="color: #099;">100</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="328" style="width: 35px; color: rgba(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="LC328" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="329" style="width: 35px; color: rgba(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="LC329" class="line" lang="c">    <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">exontable_block_end_index</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="581" style="width: 35px; color: rgba(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="581" style="width: 35px; color: rgba(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">@@ -581,19 +581,19 @@ int calc_junctions_from_cigar(fc_thread_global_context_t * global_context, int f</td>

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581

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<td class="diff-line-num new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

581

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

582

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<td class="diff-line-num new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

582

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<pre style="margin: 0;"> <span id="LC582" class="line" lang="c"></span>

</pre>

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583

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<td class="diff-line-num new_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

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<pre style="margin: 0;"> <span id="LC583" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="584" 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">

584

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<td class="diff-line-num new_line old" data-linenumber="584" 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="LC584" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="nf" style="color: #900; font-weight: 600;">unistr_cpy</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strl</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="585" style="width: 35px; color: rgba(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="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;"><span class="idiff left right">srInt_64</span></span> <span class="nf" style="color: #900; font-weight: 600;">unistr_cpy</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strl</span><span class="p">)</span></span>

</pre>

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585

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<td class="diff-line-num new_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">

585

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<pre style="margin: 0;"> <span id="LC585" class="line" lang="c"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

586

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<td class="diff-line-num new_line old" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC586" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="587" style="width: 35px; color: rgba(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="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

586

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<pre style="margin: 0;">+<span id="LC586" class="line" lang="c">    <span class="n" style="color: #333;"><span class="idiff left right">srInt_64</span></span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

587

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<td class="diff-line-num new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

587

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<pre style="margin: 0;"> <span id="LC587" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unistr_buffer_used</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strl</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unistr_buffer_size</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

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<td class="diff-line-num new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

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<pre style="margin: 0;"> <span id="LC588" class="line" lang="c">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="589" 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">

589

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<td class="diff-line-num new_line old" data-linenumber="589" 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="LC589" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unistr_buffer_size</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #099;">1000<span class="idiff left">u</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">1000u</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">1000u</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// </span>2GB</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="590" style="width: 35px; color: rgba(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="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

589

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<pre style="margin: 0;">+<span id="LC589" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unistr_buffer_size</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #099;">1000<span class="idiff left">llu</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">1000u</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">1000u</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">32</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// 3</span>2GB</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

590

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<td class="diff-line-num new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

590

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<pre style="margin: 0;"> <span id="LC590" class="line" lang="c">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

591

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<td class="diff-line-num new_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

591

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<pre style="margin: 0;"> <span id="LC591" class="line" lang="c">                    <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">unistr_buffer_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unistr_buffer_size</span> <span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">3</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

592

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<td class="diff-line-num new_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

592

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<pre style="margin: 0;"> <span id="LC592" class="line" lang="c">                    <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">unistr_buffer_space</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">realloc</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">unistr_buffer_space</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unistr_buffer_size</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

593

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<td class="diff-line-num new_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

593

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<pre style="margin: 0;"> <span id="LC593" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

594

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<td class="diff-line-num new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

594

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC594" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

595

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<td class="diff-line-num new_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

595

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<pre style="margin: 0;"> <span id="LC595" class="line" lang="c">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="596" 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">

596

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<td class="diff-line-num new_line old" data-linenumber="596" 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="LC596" class="line" lang="c">                    <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: exceed memory limit (<span class="idiff left right">4GB) for storing annotation data</span>.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC596" class="line" lang="c">                    <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: exceed memory limit (<span class="idiff left right">32GB) for storing feature names</span>.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

597

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<td class="diff-line-num new_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

597

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<pre style="margin: 0;"> <span id="LC597" class="line" lang="c">                    <span class="k" style="font-weight: 600;">return</span> <span class="mh" style="color: #099;">0xffffffffu</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

598

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<td class="diff-line-num new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

598

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<pre style="margin: 0;"> <span id="LC598" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

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<td class="diff-line-num new_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

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<pre style="margin: 0;"> <span id="LC599" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="823" style="width: 35px; color: rgba(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="823" style="width: 35px; color: rgba(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">@@ -823,12 +823,18 @@ int fc_strcmp(const void * s1, const void * s2)</td>

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823

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<td class="diff-line-num new_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

823

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<pre style="margin: 0;"> <span id="LC823" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">strcmp</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;">s1</span><span class="p">,</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;">s2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

824

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<td class="diff-line-num new_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

824

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<pre style="margin: 0;"> <span id="LC824" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

825

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<td class="diff-line-num new_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

825

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<pre style="margin: 0;"> <span id="LC825" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

826

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<pre style="margin: 0;">+<span id="LC826" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">junc_gene_free</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;">vv</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

827

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<pre style="margin: 0;">+<span id="LC827" class="line" lang="c">    <span class="n" style="color: #333;">fc_junction_gene_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vv</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

828

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<pre style="margin: 0;">+<span id="LC828" class="line" lang="c">    <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">gene_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

829

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<pre style="margin: 0;">+<span id="LC829" class="line" lang="c">    <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

830

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<pre style="margin: 0;">+<span id="LC830" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

831

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<pre style="margin: 0;">+<span id="LC831" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

826

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<td class="diff-line-num new_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

832

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<pre style="margin: 0;"> <span id="LC832" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">register_junc_feature</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">feature_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chro</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">stop</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

827

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<td class="diff-line-num new_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

833

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<pre style="margin: 0;"> <span id="LC833" class="line" lang="c">    <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gene_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">junction_features_table</span><span class="p">,</span> <span class="n" style="color: #333;">chro</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

828

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<td class="diff-line-num new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

834

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<pre style="margin: 0;"> <span id="LC834" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("REG %s : %p\n", chro, gene_table);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

829

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<td class="diff-line-num new_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

835

</td>

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<pre style="margin: 0;"> <span id="LC835" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">gene_table</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

830

</td>

<td class="diff-line-num new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

</td>

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<pre style="margin: 0;"> <span id="LC836" class="line" lang="c">            <span class="n" style="color: #333;">gene_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableCreate</span><span class="p">(</span><span class="mi" style="color: #099;">48367</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="831" 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">

831

</td>

<td class="diff-line-num new_line old" data-linenumber="837" 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="LC831" class="line" lang="c">            <span class="n" style="color: #333;">HashTableSetDeallocationFunctions</span><span class="p">(</span><span class="n" style="color: #333;">gene_table</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">free</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

837

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<pre style="margin: 0;">+<span id="LC837" class="line" lang="c">            <span class="n" style="color: #333;">HashTableSetDeallocationFunctions</span><span class="p">(</span><span class="n" style="color: #333;">gene_table</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">junc_gene_</span>free</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

832

</td>

<td class="diff-line-num new_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

838

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<pre style="margin: 0;"> <span id="LC838" class="line" lang="c">            <span class="n" style="color: #333;">HashTableSetKeyComparisonFunction</span><span class="p">(</span><span class="n" style="color: #333;">gene_table</span><span class="p">,</span> <span class="n" style="color: #333;">fc_strcmp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

833

</td>

<td class="diff-line-num new_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

839

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<pre style="margin: 0;"> <span id="LC839" class="line" lang="c">            <span class="n" style="color: #333;">HashTableSetHashFunction</span><span class="p">(</span><span class="n" style="color: #333;">gene_table</span><span class="p">,</span> <span class="n" style="color: #333;">fc_chro_hash</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

834

</td>

<td class="diff-line-num new_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

840

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC840" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="839" style="width: 35px; color: rgba(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">@@ -839,7 +845,7 @@ void register_junc_feature(fc_thread_global_context_t *global_context, char * fe</td>

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<td class="diff-line-num old_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

839

</td>

<td class="diff-line-num 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">

845

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<pre style="margin: 0;"> <span id="LC845" class="line" lang="c">    <span class="n" style="color: #333;">fc_junction_gene_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gene_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">gene_table</span><span class="p">,</span> <span class="n" style="color: #333;">feature_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

840

</td>

<td class="diff-line-num new_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

846

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC846" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">gene_info</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num 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">

841

</td>

<td class="diff-line-num new_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

847

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC847" class="line" lang="c">            <span class="n" style="color: #333;">gene_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">fc_junction_gene_t</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="842" 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">

842

</td>

<td class="diff-line-num new_line old" data-linenumber="848" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC842" class="line" lang="c">            <span class="n" style="color: #333;"><span class="idiff left">strcpy</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gene_info</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">gene_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">feature_name</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(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="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

848

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC848" class="line" lang="c">            <span class="n" style="color: #333;"><span class="idiff left">gene_info</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">gene_name</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">strdup</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">feature_name</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

843

</td>

<td class="diff-line-num new_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

849

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC849" class="line" lang="c">            <span class="n" style="color: #333;">gene_info</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">pos_first_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

844

</td>

<td class="diff-line-num new_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

850

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC850" class="line" lang="c">            <span class="n" style="color: #333;">gene_info</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">pos_last_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stop</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_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">

845

</td>

<td class="diff-line-num new_line" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

851

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC851" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="862" style="width: 35px; color: rgba(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">@@ -856,6 +862,18 @@ void free_bucket_table_list(void * pv){</td>

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<td class="diff-line-num old_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

856

</td>

<td class="diff-line-num new_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

862

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<pre style="margin: 0;"> <span id="LC862" class="line" lang="c">    <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">list</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

857

</td>

<td class="diff-line-num new_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">

863

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC863" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

858

</td>

<td class="diff-line-num new_line" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

864

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC864" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

865

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC865" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">match_feature_name_column</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">needed</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

866

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC866" 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;">ptt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

867

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC867" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">lneeded</span><span class="p">[</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">needed</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

868

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC868" class="line" lang="c">    <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">lneeded</span><span class="p">,</span> <span class="n" style="color: #333;">needed</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

869

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC869" 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;">t1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="n" style="color: #333;">lneeded</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ptt</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

870

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC870" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">t1</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

871

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC871" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">t1</span><span class="p">,</span> <span class="n" style="color: #333;">infile</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

872

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC872" class="line" lang="c">            <span class="n" style="color: #333;">t1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ptt</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

873

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC873" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

874

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC874" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

875

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC875" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(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="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

876

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC876" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

859

</td>

<td class="diff-line-num new_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

877

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC877" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define JUNCTION_BUCKET_STEP (128*1024)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

860

</td>

<td class="diff-line-num new_line" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

878

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC878" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

861

</td>

<td class="diff-line-num new_line" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

879

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC879" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">locate_junc_features</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chro</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">fc_junction_gene_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">ret_info</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_ret_info_size</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="906" style="width: 35px; color: rgba(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="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -906,10 +924,11 @@ int locate_junc_features(fc_thread_global_context_t *global_context, char * chro</td>

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<td class="diff-line-num old_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

906

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<td class="diff-line-num new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

924

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<pre style="margin: 0;"> <span id="LC924" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Memory will be allowcated in this function. The pointer is saved in *loaded_features.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

907

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<td class="diff-line-num new_line" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

925

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<pre style="margin: 0;"> <span id="LC925" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// The invoker must release the memory itself.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

908

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<td class="diff-line-num new_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

926

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<pre style="margin: 0;"> <span id="LC926" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="909" style="width: 35px; color: rgba(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="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

927

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<pre style="margin: 0;">+<span id="LC927" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_ANNOT_LINE_LENGTH 200000</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

909

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<td class="diff-line-num new_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

928

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<pre style="margin: 0;"> <span id="LC928" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">load_feature_info</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">annotation_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">file_type</span><span class="p">,</span> <span class="n" style="color: #333;">fc_feature_info_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

910

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<td class="diff-line-num new_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

929

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<pre style="margin: 0;"> <span id="LC929" class="line" lang="c"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

911

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<td class="diff-line-num new_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

930

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<pre style="margin: 0;"> <span id="LC930" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">features</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;">xk1</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;">lineno</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="912" 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">

912

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<td class="diff-line-num new_line old" data-linenumber="931" 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="LC912" 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;">file_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">MAX_LINE_LENGTH</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

931

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<pre style="margin: 0;">+<span id="LC931" 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;">file_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">MAX_<span class="idiff left right">ANNOT_</span>LINE_LENGTH</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

913

</td>

<td class="diff-line-num new_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

932

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<pre style="margin: 0;"> <span id="LC932" class="line" lang="c">    <span class="n" style="color: #333;">autozip_fp</span> <span class="n" style="color: #333;">anno_fp</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

914

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<td class="diff-line-num new_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

933

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<pre style="margin: 0;"> <span id="LC933" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">apret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">autozip_open</span><span class="p">(</span><span class="n" style="color: #333;">annotation_file</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">anno_fp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

915

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<td class="diff-line-num new_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

934

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC934" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">is_GFF_warned</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="937" style="width: 35px; color: rgba(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="956" style="width: 35px; color: rgba(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">@@ -937,8 +956,8 @@ int load_feature_info(fc_thread_global_context_t *global_context, const char * a</td>

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<td class="diff-line-num old_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

937

</td>

<td class="diff-line-num new_line" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

956

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<pre style="margin: 0;"> <span id="LC956" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// also create chro_name_table : chro_name => fc_chromosome_index_info </span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

938

</td>

<td class="diff-line-num new_line" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

957

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC957" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

939

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<td class="diff-line-num new_line" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

958

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<pre style="margin: 0;"> <span id="LC958" class="line" lang="c">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="940" 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">

940

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<td class="diff-line-num new_line old" data-linenumber="959" 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="LC940" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">//char * fgets_ret = fgets(file_line, MAX_LINE_LENGTH, fp);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="941" 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">

941

</td>

<td class="diff-line-num new_line old" data-linenumber="959" 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="LC941" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">autozip_gets</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">anno_fp</span><span class="p">,</span> <span class="n" style="color: #333;">file_line</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_LINE_LENGTH</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_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">

959

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<pre style="margin: 0;">+<span id="LC959" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">//char * fgets_ret = fgets(file_line, MAX_<span class="idiff left right">ANNOT_</span>LINE_LENGTH, fp);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

960

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<pre style="margin: 0;">+<span id="LC960" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">autozip_gets</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">anno_fp</span><span class="p">,</span> <span class="n" style="color: #333;">file_line</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_<span class="idiff left right">ANNOT_</span>LINE_LENGTH</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

942

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<td class="diff-line-num new_line" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

961

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<pre style="margin: 0;"> <span id="LC961" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">token_temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chro_name</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

943

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<td class="diff-line-num new_line" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

962

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<pre style="margin: 0;"> <span id="LC962" class="line" lang="c">            <span class="n" style="color: #333;">fc_chromosome_index_info</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chro_stab</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

944

</td>

<td class="diff-line-num new_line" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

963

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<pre style="margin: 0;"> <span id="LC963" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">feature_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="951" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -951,7 +970,7 @@ int load_feature_info(fc_thread_global_context_t *global_context, const char * a</td>

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<td class="diff-line-num old_line" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

951

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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="n" style="color: #333;">chro_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="n" style="color: #333;">file_line</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_temp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

952

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<td class="diff-line-num new_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

971

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<pre style="margin: 0;"> <span id="LC971" class="line" lang="c">                    <span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_temp</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// lib_name (not needed)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

953

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<td class="diff-line-num new_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

972

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<pre style="margin: 0;"> <span id="LC972" 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;">feature_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_temp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="954" 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">

954

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<td class="diff-line-num new_line old" data-linenumber="973" 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="LC954" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">strcmp</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">feature_type</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">global_context</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">feature_name_column</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="955" style="width: 35px; color: rgba(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="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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">match_feature_name_column</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">feature_type</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">global_context</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">feature_name_column</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num 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">

955

</td>

<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="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

956

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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="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_temp</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// feature_start</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

957

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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="n" style="color: #333;">feature_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_temp</span><span class="p">));</span><span class="c1" style="color: #998; font-style: italic;">// feature_end</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1004" style="width: 35px; color: rgba(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="1023" style="width: 35px; color: rgba(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">@@ -1004,8 +1023,12 @@ int load_feature_info(fc_thread_global_context_t *global_context, const char * a</td>

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<td class="diff-line-num old_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1004

</td>

<td class="diff-line-num new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1023

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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="c">   <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1005

</td>

<td class="diff-line-num new_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1024

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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="c">   <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1006

</td>

<td class="diff-line-num new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1025

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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">is_gene_id_found</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1007" 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">

1007

</td>

<td class="diff-line-num new_line old" data-linenumber="1026" 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="LC1007" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">autozip_gets</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">anno_fp</span><span class="p">,</span> <span class="n" style="color: #333;">file_line</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_LINE_LENGTH</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1008" style="width: 35px; color: rgba(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="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1026

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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rchars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">autozip_gets</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">anno_fp</span><span class="p">,</span> <span class="n" style="color: #333;">file_line</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_<span class="idiff left right">ANNOT_</span>LINE_LENGTH</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1008

</td>

<td class="diff-line-num new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1027

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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rchars</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1009" style="width: 35px; color: rgba(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="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1028

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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rchars</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">MAX_ANNOT_LINE_LENGTH</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1009" style="width: 35px; color: rgba(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="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1029

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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADprintf</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;">ERROR: the %u-th line in your GTF file is extremely long (longer than %d bytes).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">The program cannot parse this line.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">lineno</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;">MAX_ANNOT_LINE_LENGTH</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1009" style="width: 35px; color: rgba(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="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1030

</td>

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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="c">                   <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1009" style="width: 35px; color: rgba(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="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1031

</td>

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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1009

</td>

<td class="diff-line-num new_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1032

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1032" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1010

</td>

<td class="diff-line-num new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1033

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1033" class="line" lang="c">           <span class="n" style="color: #333;">lineno</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1011

</td>

<td class="diff-line-num new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1034

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1034" 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;">token_temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1018" style="width: 35px; color: rgba(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="1041" style="width: 35px; color: rgba(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">@@ -1018,9 +1041,12 @@ int load_feature_info(fc_thread_global_context_t *global_context, const char * a</td>

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<td class="diff-line-num old_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1018

</td>

<td class="diff-line-num new_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1041

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1041" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1019

</td>

<td class="diff-line-num new_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1042

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1042" 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;">feature_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="n" style="color: #333;">file_line</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_temp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1020

</td>

<td class="diff-line-num new_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1043

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1043" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">feature_name_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">feature_name</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1021" 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">

1021

</td>

<td class="diff-line-num new_line old" data-linenumber="1044" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1021" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">feature_name_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span><span class="p">)</span> <span class="n" style="color: #333;">feature_name</span><span class="p">[</span><span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1022" style="width: 35px; color: rgba(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="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1044

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1044" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">feature_name_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1022" style="width: 35px; color: rgba(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="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1045

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1045" class="line" lang="c">                           <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"WARNING: feature name on the %d-th line is longer than %d bytes. The name is truncated</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">lineno</span><span class="p">,</span> <span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1022" style="width: 35px; color: rgba(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="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1046

</td>

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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="c">                           <span class="n" style="color: #333;">feature_name</span><span class="p">[</span><span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1022" style="width: 35px; color: rgba(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="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1047

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1047" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1022

</td>

<td class="diff-line-num new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1048

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1048" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1023" 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">

1023

</td>

<td class="diff-line-num new_line old" data-linenumber="1049" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1023" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">genename_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unistr_cpy</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</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;">feature_name</span><span class="p">,</span> <span class="n" style="color: #333;">feature_name_len</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1024" style="width: 35px; color: rgba(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="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1049

</td>

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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="c">                   <span class="n" style="color: #333;"><span class="idiff left right">srInt_64</span></span> <span class="n" style="color: #333;">genename_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unistr_cpy</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</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;">feature_name</span><span class="p">,</span> <span class="n" style="color: #333;">feature_name_len</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1024

</td>

<td class="diff-line-num new_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1050

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1050" class="line" lang="c">                   </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1025

</td>

<td class="diff-line-num new_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1051

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1051" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//          SUBREADprintf("REALL: '%s'=%d  [%d] %p  POS=%d\t\tOLD_NAME_POS=%d\n" , feature_name, feature_name_len , xk1, ret_features+xk1, genename_pos, xk1>0?ret_features[xk1-1].feature_name_pos:-1);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1026

</td>

<td class="diff-line-num new_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1052

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1052" class="line" lang="c">                   <span class="n" style="color: #333;">ret_features</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">].</span><span class="n" style="color: #333;">feature_name_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genename_pos</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1028" style="width: 35px; color: rgba(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="1054" style="width: 35px; color: rgba(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">@@ -1028,7 +1054,7 @@ int load_feature_info(fc_thread_global_context_t *global_context, const char * a</td>

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<td class="diff-line-num old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1028

</td>

<td class="diff-line-num new_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1054

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<pre style="margin: 0;"> <span id="LC1054" 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;">seq_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_temp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1029

</td>

<td class="diff-line-num new_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1055

</td>

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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chro_name_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">seq_name</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1030

</td>

<td class="diff-line-num new_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1056

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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">chro_name_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">CHROMOSOME_NAME_LENGTH</span><span class="p">)</span> <span class="n" style="color: #333;">seq_name</span><span class="p">[</span><span class="n" style="color: #333;">CHROMOSOME_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1031" 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">

1031

</td>

<td class="diff-line-num new_line old" data-linenumber="1057" 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="LC1031" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">chro_name_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unistr_cpy</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</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;">seq_name</span><span class="p">,</span> <span class="n" style="color: #333;">chro_name_len</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1032" style="width: 35px; color: rgba(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="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1057

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1057" class="line" lang="c">                   <span class="n" style="color: #333;"><span class="idiff left right">srInt_64</span></span> <span class="n" style="color: #333;">chro_name_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unistr_cpy</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</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;">seq_name</span><span class="p">,</span> <span class="n" style="color: #333;">chro_name_len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1032

</td>

<td class="diff-line-num new_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1058

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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="c">                   <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">longest_chro_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">chro_name_len</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">longest_chro_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1033

</td>

<td class="diff-line-num new_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1059

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1059" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1034

</td>

<td class="diff-line-num new_line" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1060

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1060" class="line" lang="c"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1125" style="width: 35px; color: rgba(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="1151" style="width: 35px; color: rgba(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">@@ -1125,7 +1151,7 @@ int load_feature_info(fc_thread_global_context_t *global_context, const char * a</td>

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<td class="diff-line-num old_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1125

</td>

<td class="diff-line-num new_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1151

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<pre style="margin: 0;"> <span id="LC1151" 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;">seq_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="n" style="color: #333;">file_line</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_temp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1126

</td>

<td class="diff-line-num new_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1152

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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="c">                   <span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_temp</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">// source</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1127

</td>

<td class="diff-line-num new_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1153

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<pre style="margin: 0;"> <span id="LC1153" 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;">feature_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtok_r</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_temp</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">// feature_type</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1128" 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">

1128

</td>

<td class="diff-line-num new_line old" data-linenumber="1154" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1128" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">strcmp</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">feature_type</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">global_context</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">feature_name_column</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1129" style="width: 35px; color: rgba(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="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1154

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1154" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">match_feature_name_column</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">feature_type</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">global_context</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">feature_name_column</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1129

</td>

<td class="diff-line-num new_line" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1155

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1155" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1130

</td>

<td class="diff-line-num new_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1156

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1156" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">xk1</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">ret_features_size</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1131

</td>

<td class="diff-line-num new_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1157

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<pre style="margin: 0;"> <span id="LC1157" class="line" lang="c">                                   <span class="n" style="color: #333;">ret_features_size</span> <span class="o" style="font-weight: 600;">*=</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1221" style="width: 35px; color: rgba(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="1247" style="width: 35px; color: rgba(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">@@ -1221,12 +1247,15 @@ int load_feature_info(fc_thread_global_context_t *global_context, const char * a</td>

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<td class="diff-line-num new_line" data-linenumber="1247" style="width: 35px; color: rgba(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="LC1247" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1248" style="width: 35px; color: rgba(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="LC1248" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1249" style="width: 35px; color: rgba(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="LC1249" class="line" lang="c">                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">feature_name_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">feature_name_tmp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1224" 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">

1224

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<td class="diff-line-num new_line old" data-linenumber="1250" 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="LC1224" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">feature_name_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span><span class="p">)</span> <span class="n" style="color: #333;">feature_name_tmp</span><span class="p">[</span><span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1225" style="width: 35px; color: rgba(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="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">feature_name_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1225" style="width: 35px; color: rgba(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="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1251

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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="c">                                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"WARNING: feature name on the %d-th line is longer than %d bytes. The name is truncated</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">lineno</span><span class="p">,</span> <span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1225" style="width: 35px; color: rgba(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="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1252

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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="c">                                   <span class="n" style="color: #333;">feature_name_tmp</span><span class="p">[</span><span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1225" style="width: 35px; color: rgba(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="1253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1225

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<td class="diff-line-num new_line" data-linenumber="1254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1254

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<pre style="margin: 0;"> <span id="LC1254" class="line" lang="c">                           <span class="n" style="color: #333;">ret_features</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">].</span><span class="n" style="color: #333;">feature_name_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unistr_cpy</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</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;">feature_name_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">feature_name_len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1226

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<td class="diff-line-num new_line" data-linenumber="1255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1255

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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1256

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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="c">                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chro_name_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">seq_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1257

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<pre style="margin: 0;"> <span id="LC1257" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">chro_name_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">CHROMOSOME_NAME_LENGTH</span><span class="p">)</span> <span class="n" style="color: #333;">seq_name</span><span class="p">[</span><span class="n" style="color: #333;">CHROMOSOME_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1229" 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">

1229

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<td class="diff-line-num new_line old" data-linenumber="1258" 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="LC1229" class="line" lang="c">                           <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">chro_name_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unistr_cpy</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</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;">seq_name</span><span class="p">,</span> <span class="n" style="color: #333;">chro_name_len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1230" style="width: 35px; color: rgba(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="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1258

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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="c">                           <span class="n" style="color: #333;"><span class="idiff left right">srInt_64</span></span> <span class="n" style="color: #333;">chro_name_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unistr_cpy</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</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;">seq_name</span><span class="p">,</span> <span class="n" style="color: #333;">chro_name_len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1230" style="width: 35px; color: rgba(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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1259

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<pre style="margin: 0;"> <span id="LC1259" class="line" lang="c">                           <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">longest_chro_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">chro_name_len</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">longest_chro_name</span><span class="p">);</span></span>

</pre>

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1231

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<td class="diff-line-num new_line" data-linenumber="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1260

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<pre style="margin: 0;"> <span id="LC1260" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1232

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<td class="diff-line-num new_line" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1261

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<pre style="margin: 0;"> <span id="LC1261" class="line" lang="c">                           <span class="n" style="color: #333;">ret_features</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">].</span><span class="n" style="color: #333;">chro_name_pos_delta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chro_name_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ret_features</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">].</span><span class="n" style="color: #333;">feature_name_pos</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3991" style="width: 35px; color: rgba(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="4020" style="width: 35px; color: rgba(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">@@ -3991,7 +4020,7 @@ void vote_and_add_count(fc_thread_global_context_t * global_context, fc_thread_t</td>

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<td class="diff-line-num old_line" data-linenumber="3991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3991

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4020

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<pre style="margin: 0;"> <span id="LC4020" class="line" lang="c">                                                   <span class="n" style="color: #333;">add_scRNA_read_to_pool</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">thread_context</span><span class="p">,</span> <span class="n" style="color: #333;">assignment_target_number</span><span class="p">,</span> <span class="n" style="color: #333;">read_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3992

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<td class="diff-line-num new_line" data-linenumber="4021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4021

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<pre style="margin: 0;"> <span id="LC4021" class="line" lang="c">                                           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3993

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<td class="diff-line-num new_line" data-linenumber="4022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4022

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<pre style="margin: 0;"> <span id="LC4022" 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;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_multi_overlap_allowed</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3994" 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">

3994

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<td class="diff-line-num new_line old" data-linenumber="4023" 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="LC3994" class="line" lang="c">                                           <span class="cp" style="color: #999; font-weight: 600;">#define GENE_NAME_LIST_BUFFER_SIZE <span class="idiff left right">5000</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3995" style="width: 35px; color: rgba(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="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4023" class="line" lang="c">                                           <span class="cp" style="color: #999; font-weight: 600;">#define GENE_NAME_LIST_BUFFER_SIZE <span class="idiff left right">(FEATURE_NAME_LENGTH * 50) </span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3995

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<td class="diff-line-num new_line" data-linenumber="4024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4024

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<pre style="margin: 0;"> <span id="LC4024" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3996

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<td class="diff-line-num new_line" data-linenumber="4025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4025

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<pre style="margin: 0;"> <span id="LC4025" class="line" lang="c">                                           <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">final_feture_names</span><span class="p">[</span><span class="n" style="color: #333;">GENE_NAME_LIST_BUFFER_SIZE</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3997

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<td class="diff-line-num new_line" data-linenumber="4026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4026

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<pre style="margin: 0;"> <span id="LC4026" class="line" lang="c">                                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">assigned_no</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;">xk1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4118" style="width: 35px; color: rgba(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="4147" style="width: 35px; color: rgba(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">@@ -4118,7 +4147,7 @@ void scRNA_merge_thread_umitables(void *ky, void *val, HashTable * tab){</td>

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<td class="diff-line-num old_line" data-linenumber="4118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4118

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<td class="diff-line-num new_line" data-linenumber="4147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4147

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<pre style="margin: 0;"> <span id="LC4147" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4119

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<td class="diff-line-num new_line" data-linenumber="4148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4148

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<pre style="margin: 0;"> <span id="LC4148" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4120

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<td class="diff-line-num new_line" data-linenumber="4149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4149

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<pre style="margin: 0;"> <span id="LC4149" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MIN_EXPRESSED_UMIS_PER_CELL 100 </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4121" 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">

4121

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<td class="diff-line-num new_line old" data-linenumber="4150" 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="LC4121" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MIN_EXPRESSED_UMIS_PER_GENE <span class="idiff left right">3</span> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4122" style="width: 35px; color: rgba(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="4150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4150

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<pre style="margin: 0;">+<span id="LC4150" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MIN_EXPRESSED_UMIS_PER_GENE <span class="idiff left right">(3-2)</span> </span></span>

</pre>

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4122

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<td class="diff-line-num new_line" data-linenumber="4151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4151

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<pre style="margin: 0;"> <span id="LC4151" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4123

</td>

<td class="diff-line-num new_line" data-linenumber="4152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4152

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<pre style="margin: 0;"> <span id="LC4152" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merge_write_copy_gene_nos</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;">ky</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;">va</span> <span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tab</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4124

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<td class="diff-line-num new_line" data-linenumber="4153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4153

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<pre style="margin: 0;"> <span id="LC4153" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">used_gene_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4127" style="width: 35px; color: rgba(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="4156" style="width: 35px; color: rgba(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">@@ -4127,10 +4156,10 @@ void scRNA_merge_write_copy_gene_nos(void * ky, void * va , HashTable *tab){</td>

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<td class="diff-line-num old_line" data-linenumber="4127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4127

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<td class="diff-line-num new_line" data-linenumber="4156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4156

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<pre style="margin: 0;"> <span id="LC4156" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">UMIs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">used_gene_table</span><span class="p">,</span> <span class="n" style="color: #333;">ky</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4128

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<td class="diff-line-num new_line" data-linenumber="4157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4157

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<pre style="margin: 0;"> <span id="LC4157" class="line" lang="c">   <span class="n" style="color: #333;">HashTablePut</span><span class="p">(</span><span class="n" style="color: #333;">used_gene_table</span><span class="p">,</span> <span class="n" style="color: #333;">ky</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">UMIs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">one_sampl_gene_to_cell_umis</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4129

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<td class="diff-line-num new_line" data-linenumber="4158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4158

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<pre style="margin: 0;"> <span id="LC4158" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4130" 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">

4130

</td>

<td class="diff-line-num new_line old" data-linenumber="4159" 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="LC4130" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merge_write_zero_gene</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">linebuf</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">used_cell_barcode</span>_list</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4131" style="width: 35px; color: rgba(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="4159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4159

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4159" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merge_write_zero_gene</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">linebuf</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">high_confid_barcode_index</span>_list</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4131

</td>

<td class="diff-line-num new_line" data-linenumber="4160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4160

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<pre style="margin: 0;"> <span id="LC4160" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4132

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<td class="diff-line-num new_line" data-linenumber="4161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4161

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4161" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">x1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4133" 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">

4133

</td>

<td class="diff-line-num new_line old" data-linenumber="4162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4133" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">used_cell_barcode</span>_list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="p">;</span><span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">linebuf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ret</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4134" style="width: 35px; color: rgba(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="4162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4162

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4162" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">high_confid_barcode_index</span>_list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="p">;</span><span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">linebuf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ret</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4134

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<td class="diff-line-num new_line" data-linenumber="4163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4163

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<pre style="margin: 0;"> <span id="LC4163" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4135

</td>

<td class="diff-line-num new_line" data-linenumber="4164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4164

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4164" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4136

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<td class="diff-line-num new_line" data-linenumber="4165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4165

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<pre style="margin: 0;"> <span id="LC4165" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4259" style="width: 35px; color: rgba(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="4288" style="width: 35px; color: rgba(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">@@ -4259,7 +4288,7 @@ ArrayList * scRNA_reduce_cellno_umino_p1_list(fc_thread_global_context_t * globa</td>

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<td class="diff-line-num old_line" data-linenumber="4259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4259

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<td class="diff-line-num new_line" data-linenumber="4288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4288

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<pre style="margin: 0;"> <span id="LC4288" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4260

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<td class="diff-line-num new_line" data-linenumber="4289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4289

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<pre style="margin: 0;"> <span id="LC4289" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4261

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<td class="diff-line-num new_line" data-linenumber="4290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4290

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<pre style="margin: 0;"> <span id="LC4290" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4262" 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">

4262

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<td class="diff-line-num new_line old" data-linenumber="4291" 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="LC4262" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_write_a_gene</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span>  <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span> <span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">used_cell_barcode_tabs</span> <span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;"><span class="idiff left right">used_cell_barcode</span>_list</span> <span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">umi_merged_list</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gen_no_list</span><span class="p">,</span>  <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">used_gene_i</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">linebuf</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4263" style="width: 35px; color: rgba(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="4291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4291

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<pre style="margin: 0;">+<span id="LC4291" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_write_a_gene</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span>  <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span> <span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">used_cell_barcode_tabs</span> <span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;"><span class="idiff left right">high_confid_barcode_index</span>_list</span> <span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">umi_merged_list</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gen_no_list</span><span class="p">,</span>  <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">used_gene_i</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">linebuf</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4263

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<td class="diff-line-num new_line" data-linenumber="4292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4292

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<pre style="margin: 0;"> <span id="LC4292" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">gene_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">gen_no_list</span><span class="p">,</span> <span class="n" style="color: #333;">used_gene_i</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4264

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<td class="diff-line-num new_line" data-linenumber="4293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4293

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<pre style="margin: 0;"> <span id="LC4293" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">line_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_gene_level</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">gene_no</span> <span class="o" style="font-weight: 600;">:</span>  <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">lineno_2_sortedno_tab</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gene_no</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// convert line_no to sorted_order</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4265

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<td class="diff-line-num new_line" data-linenumber="4294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4294

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<pre style="margin: 0;"> <span id="LC4294" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">linebuf_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4278" style="width: 35px; color: rgba(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="4307" style="width: 35px; color: rgba(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">@@ -4278,12 +4307,12 @@ int scRNA_merged_write_a_gene(fc_thread_global_context_t * global_context,  Hash</td>

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<td class="diff-line-num old_line" data-linenumber="4278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4278

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<td class="diff-line-num new_line" data-linenumber="4307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4307

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<pre style="margin: 0;"> <span id="LC4307" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_sample_sheet_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4279

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<td class="diff-line-num new_line" data-linenumber="4308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4308

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4308" class="line" lang="c">           <span class="n" style="color: #333;">ArrayList</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cellno_umino_p1_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gene_no</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4280

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<td class="diff-line-num new_line" data-linenumber="4309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4309

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4309" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cellno_umino_p1_list</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4281" 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">

4281

</td>

<td class="diff-line-num new_line old" data-linenumber="4310" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4281" class="line" lang="c">                   <span class="n" style="color: #333;">linebuf_ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">scRNA_merge_write_zero_gene</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">linebuf</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">linebuf_ptr</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">used_cell_barcode</span>_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4282" style="width: 35px; color: rgba(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="4310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4310

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4310" class="line" lang="c">                   <span class="n" style="color: #333;">linebuf_ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">scRNA_merge_write_zero_gene</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">linebuf</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">linebuf_ptr</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">high_confid_barcode_index</span>_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4282

</td>

<td class="diff-line-num new_line" data-linenumber="4311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4311

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4311" class="line" lang="c">           <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4283

</td>

<td class="diff-line-num new_line" data-linenumber="4312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4312

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4312" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tab_cell_ptr</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;">used_cell_bc_ptr</span> <span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4284

</td>

<td class="diff-line-num new_line" data-linenumber="4313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4313

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4313" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4285" 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">

4285

</td>

<td class="diff-line-num new_line old" data-linenumber="4314" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4285" class="line" lang="c">                   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_bc_ptr</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;">used_cell_bc_ptr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left right">used_cell_barcode</span>_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">used_cell_bc_ptr</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4286" 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">

4286

</td>

<td class="diff-line-num new_line old" data-linenumber="4314" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4286" class="line" lang="c">                           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">used_cell_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">used_cell_barcode</span>_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">used_cell_bc_ptr</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4287" style="width: 35px; color: rgba(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="4314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4314

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4314" class="line" lang="c">                   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_bc_ptr</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;">used_cell_bc_ptr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left right">high_confid_barcode_index</span>_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">used_cell_bc_ptr</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4287" style="width: 35px; color: rgba(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="4315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4315

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4315" class="line" lang="c">                           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">used_cell_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">high_confid_barcode_index</span>_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">used_cell_bc_ptr</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4287

</td>

<td class="diff-line-num new_line" data-linenumber="4316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4316

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4316" class="line" lang="c"></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="4288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4288

</td>

<td class="diff-line-num new_line" data-linenumber="4317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4317

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4317" class="line" lang="c">                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">write_cnt</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4289

</td>

<td class="diff-line-num new_line" data-linenumber="4318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4318

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4318" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tab_cell_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cellno_umino_p1_list</span> <span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="p">)</span><span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4308" style="width: 35px; color: rgba(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="4337" style="width: 35px; color: rgba(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">@@ -4308,73 +4337,282 @@ int scRNA_merged_write_a_gene(fc_thread_global_context_t * global_context,  Hash</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4308

</td>

<td class="diff-line-num new_line" data-linenumber="4337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4337

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4337" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">total_count_in_row</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4309

</td>

<td class="diff-line-num new_line" data-linenumber="4338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4338

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4338" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4310

</td>

<td class="diff-line-num new_line" data-linenumber="4339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4339

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4339" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4311" 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">

4311

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<td class="diff-line-num new_line old" data-linenumber="4340" 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="LC4311" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// this function writes a single count table.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4312" 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">

4312

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<td class="diff-line-num new_line old" data-linenumber="4340" 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="LC4312" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Rows: genes</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4313" 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">

4313

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<td class="diff-line-num new_line old" data-linenumber="4340" 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="LC4313" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Cols: Cell_Barcode +"."+ SampleName</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4314" 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">

4314

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<td class="diff-line-num new_line old" data-linenumber="4340" 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="LC4314" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_to_tables_write</span><span class="p">(</span> <span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span> <span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">used_cell_barcode_tabs</span> <span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_umi_list</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4315" 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">

4315

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<td class="diff-line-num new_line old" data-linenumber="4340" 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="LC4315" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ofname</span><span class="p">[</span><span class="n" style="color: #333;">MAX_FILE_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">20</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4316" 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">

4316

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<td class="diff-line-num new_line old" data-linenumber="4340" 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="LC4316" class="line" lang="c">   <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofname</span><span class="p">,</span><span class="s" style="color: #d14;">"%s.scRNA.table"</span><span class="p">,</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_file_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4317" 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">

4317

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<td class="diff-line-num new_line old" data-linenumber="4340" 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="LC4317" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ofp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span> <span class="n" style="color: #333;">ofname</span> <span class="p">,</span> <span class="s" style="color: #d14;">"w"</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4318" 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">

4318

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<td class="diff-line-num new_line old" data-linenumber="4340" 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="LC4318" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="n" style="color: #333;">cell_items_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4319" 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">

4319

</td>

<td class="diff-line-num new_line old" data-linenumber="4340" 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="LC4319" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">xkk</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4320" 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">

4320

</td>

<td class="diff-line-num new_line old" data-linenumber="4340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4320" class="line" lang="c">   <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">used_cell_barcode_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</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;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_sample_sheet_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4340

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<pre style="margin: 0;">+<span id="LC4340" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SCRNA_AMBIENT_RESCURE_MEDIAN_FRACTION 0.01</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4341

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<pre style="margin: 0;">+<span id="LC4341" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_ambient_rescure</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_gene_to_cell_umis_tab</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">used_cell_barcode_tab</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">this_sample_ambient_rescure_candi</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">this_sample_45k_90k_barcode_idx</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">highconf_list</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4342

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4342" class="line" lang="c">   <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sorted_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableSortedIndexes</span><span class="p">(</span> <span class="n" style="color: #333;">used_cell_barcode_tab</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4343

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<pre style="margin: 0;">+<span id="LC4343" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">highconf_list_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListToLookupTable_Int</span><span class="p">(</span><span class="n" style="color: #333;">highconf_list</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4344

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<pre style="margin: 0;">+<span id="LC4344" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">x1</span><span class="p">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4345" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sorted_idx</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4346

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<pre style="margin: 0;">+<span id="LC4346" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">this_bc_pnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">sorted_idx</span> <span class="p">,</span>  <span class="n" style="color: #333;">x1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4347" 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;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">highconf_list_tab</span><span class="p">,</span> <span class="n" style="color: #333;">this_bc_pnt</span><span class="p">))</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// assuming that all high-umi barcodes are high-confident, this makes x1 being the # of total high-confidence barcodes.    </span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4348" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4349" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4350" class="line" lang="c">           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">median_umis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcode_tab</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">sorted_idx</span> <span class="p">,</span>  <span class="p">(</span><span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4351

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<pre style="margin: 0;">+<span id="LC4351" class="line" lang="c">           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">median_umis_001_cut</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">srInt_64</span><span class="p">)(</span><span class="n" style="color: #333;">median_umis</span> <span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1</span><span class="p">.</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">SCRNA_AMBIENT_RESCURE_MEDIAN_FRACTION</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4352

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<pre style="margin: 0;">+<span id="LC4352" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("MEDIANTEST : X1 = %lld, MID = %lld, MID_CUT = %lld\n", x1, median_umis, median_umis_001_cut);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4353

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<pre style="margin: 0;">+<span id="LC4353" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sorted_idx</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4354

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<pre style="margin: 0;">+<span id="LC4354" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">this_bc_pnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">sorted_idx</span> <span class="p">,</span>  <span class="n" style="color: #333;">x1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4355

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<pre style="margin: 0;">+<span id="LC4355" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">highconf_list_tab</span><span class="p">,</span> <span class="n" style="color: #333;">this_bc_pnt</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// it is in high-conf list</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4356

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<pre style="margin: 0;">+<span id="LC4356" class="line" lang="c">                   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">this_bc_umis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcode_tab</span><span class="p">,</span> <span class="n" style="color: #333;">this_bc_pnt</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4357

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4357" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">this_bc_umis</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">median_umis_001_cut</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4358

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<pre style="margin: 0;">+<span id="LC4358" class="line" lang="c">                   <span class="n" style="color: #333;">ArrayListPush</span><span class="p">(</span><span class="n" style="color: #333;">this_sample_ambient_rescure_candi</span><span class="p">,</span> <span class="n" style="color: #333;">this_bc_pnt</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4359

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4359" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4360

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4360" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4361

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4361" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">45000</span><span class="p">;</span> <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sorted_idx</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4362

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4362" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">90000</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4363

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4363" class="line" lang="c">           <span class="n" style="color: #333;">ArrayListPush</span><span class="p">(</span><span class="n" style="color: #333;">this_sample_45k_90k_barcode_idx</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">sorted_idx</span> <span class="p">,</span>  <span class="n" style="color: #333;">x1</span><span class="p">)</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4364

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4364" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4365

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4365" class="line" lang="c">   <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">sorted_idx</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4366

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4366" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("AMBIENT_CANDIDATES = %lld   45K-90K = %lld\n", this_sample_ambient_rescure_candi -> numOfElements, this_sample_45k_90k_barcode_idx-> numOfElements);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4367

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4367" class="line" lang="c">   <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">highconf_list_tab</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4321" style="width: 35px; color: rgba(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="4368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4368

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4368" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4321

</td>

<td class="diff-line-num new_line" data-linenumber="4369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4369

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4369" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4322" 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">

4322

</td>

<td class="diff-line-num new_line old" data-linenumber="4370" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4322" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_gene_level</span><span class="o" style="font-weight: 600;">?</span><span class="s" style="color: #d14;">"Geneid"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"FeatureNo"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4323" 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">

4323

</td>

<td class="diff-line-num new_line old" data-linenumber="4370" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4323" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_sample_sheet_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4324" 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">

4324

</td>

<td class="diff-line-num new_line old" data-linenumber="4370" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4324" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//             SUBREADprintf("CELL BARCODE USED TAB = %ld  ; GENE_TO_CELL&UMI TAB = %ld ; for %d sample\n", used_cell_barcode_tabs[x1]-> numOfElements, merged_tables_gene_to_cell_umis[x1]-> numOfElements, x1);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4325" 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">

4325

</td>

<td class="diff-line-num new_line old" data-linenumber="4370" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4325" class="line" lang="c">           <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">raw_used_cells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableKeys</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcode_tabs</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4326" 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">

4326

</td>

<td class="diff-line-num new_line old" data-linenumber="4370" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4326" class="line" lang="c">           <span class="n" style="color: #333;">ArrayListSort</span><span class="p">(</span><span class="n" style="color: #333;">raw_used_cells</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4327" 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">

4327

</td>

<td class="diff-line-num new_line old" data-linenumber="4370" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4327" class="line" lang="c">           <span class="n" style="color: #333;">used_cell_barcode_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListCreate</span><span class="p">(</span><span class="n" style="color: #333;">raw_used_cells</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4328" 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">

4328

</td>

<td class="diff-line-num new_line old" data-linenumber="4370" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4328" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">xkk</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;">xkk</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">raw_used_cells</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">xkk</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4329" 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">

4329

</td>

<td class="diff-line-num new_line old" data-linenumber="4370" 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="LC4329" class="line" lang="c">                   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">cell_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">raw_used_cells</span><span class="p">,</span> <span class="n" style="color: #333;">xkk</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4330" 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">

4330

</td>

<td class="diff-line-num new_line old" data-linenumber="4370" 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="LC4330" class="line" lang="c">                   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">umis_of_cell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcode_tabs</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cell_no</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4331" 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">

4331

</td>

<td class="diff-line-num new_line old" data-linenumber="4370" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4331" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">umis_of_cell</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">MIN_EXPRESSED_UMIS_PER_CELL</span><span class="p">)</span> <span class="n" style="color: #333;">ArrayListPush</span><span class="p">(</span> <span class="n" style="color: #333;">used_cell_barcode_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cell_no</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4370

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4370" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4371

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4371" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SCRNA_BOOTSTRAP_HIGH_INDEX 30</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4372

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4372" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SCRNA_BOOTSTRAP_SAMPLING_TIMES 100</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4373

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4373" class="line" lang="c"></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="4332" style="width: 35px; color: rgba(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="4374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4374

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4374" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_bootstrap_a_sample</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_gene_to_cell_umis_tab</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">used_cell_barcode_tab</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_umi_list</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">highconf_list</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4375

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4375" class="line" lang="c">   <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sorted_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableSortedIndexes</span><span class="p">(</span> <span class="n" style="color: #333;">used_cell_barcode_tab</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4376

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4376" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">UMIs_30th_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcode_tab</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">sorted_idx</span> <span class="p">,</span>  <span class="n" style="color: #333;">SCRNA_BOOTSTRAP_HIGH_INDEX</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">))</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4377

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4377" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4378

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4378" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4379

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4379" class="line" lang="c">           <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"HIGHEST 30 TH UMIs = %lld</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">UMIs_30th_high</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4380

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<pre style="margin: 0;">+<span id="LC4380" class="line" lang="c">           <span class="n" style="color: #333;">UMIs_30th_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcode_tab</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">sorted_idx</span> <span class="p">,</span>  <span class="n" style="color: #333;">SCRNA_BOOTSTRAP_HIGH_INDEX</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">0</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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4381

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4381" class="line" lang="c">           <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"HIGHEST 31 TH UMIs = %lld</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">UMIs_30th_high</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4382

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<pre style="margin: 0;">+<span id="LC4382" class="line" lang="c">           <span class="n" style="color: #333;">UMIs_30th_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcode_tab</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">sorted_idx</span> <span class="p">,</span>  <span class="n" style="color: #333;">SCRNA_BOOTSTRAP_HIGH_INDEX</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span> <span class="p">))</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4383

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4383" class="line" lang="c">           <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"HIGHEST 29 TH UMIs = %lld</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">UMIs_30th_high</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4384

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4384" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4385

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4385" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4386

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4386" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">x2</span><span class="p">,</span><span class="n" style="color: #333;">x1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4387

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4387" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">this_total</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4388

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4388" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">SCRNA_BOOTSTRAP_SAMPLING_TIMES</span><span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4389

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4389" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x2</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;">x2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sorted_idx</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="p">;</span> <span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4390

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4390" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">barcode_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListRandom</span><span class="p">(</span><span class="n" style="color: #333;">sorted_idx</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4332" style="width: 35px; color: rgba(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="4391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4391

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4391" class="line" lang="c">                   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">this_umis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span> <span class="n" style="color: #333;">used_cell_barcode_tab</span><span class="p">,</span> <span class="n" style="color: #333;">barcode_idx</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>

</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="4332" style="width: 35px; color: rgba(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="4392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4392

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4392" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">this_umis</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">UMIs_30th_high</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="n" style="color: #333;">this_total</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4332

</td>

<td class="diff-line-num new_line" data-linenumber="4393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4393

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4393" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4333" 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">

4333

</td>

<td class="diff-line-num new_line old" data-linenumber="4394" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4333" class="line" lang="c">           <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">raw_used_cells</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4334" 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">

4334

</td>

<td class="diff-line-num new_line old" data-linenumber="4394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4334" 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;">sample_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_sample_id_to_name</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4394

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<pre style="margin: 0;">+<span id="LC4394" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4335" style="width: 35px; color: rgba(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="4395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4395

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<pre style="margin: 0;">+<span id="LC4395" class="line" lang="c">   <span class="n" style="color: #333;">this_total</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">SCRNA_BOOTSTRAP_SAMPLING_TIMES</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4335" style="width: 35px; color: rgba(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="4396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4396

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4396" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"FINAL SELECTION_IDX =  %lld</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">this_total</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4335" style="width: 35px; color: rgba(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="4397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4397

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<pre style="margin: 0;">+<span id="LC4397" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">sorted_idx</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">,</span> <span class="n" style="color: #333;">this_total</span><span class="p">)</span> <span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">ArrayListPush</span><span class="p">(</span><span class="n" style="color: #333;">highconf_list</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span> <span class="n" style="color: #333;">sorted_idx</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4398

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4398" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4335" style="width: 35px; color: rgba(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="4399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4399

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4399" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4335" style="width: 35px; color: rgba(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="4400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4400

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<pre style="margin: 0;">+<span id="LC4400" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">build_exon_name</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">fc_feature_info_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">exon_name</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4335" style="width: 35px; color: rgba(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="4401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4401

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4401" class="line" lang="c">    <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">exon_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s:fc,spl:%s:fc,spl:%u:fc,spl:%u:fc,spl:%c"</span><span class="p">,</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">unistr_buffer_space</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">feature_name_pos</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4335" style="width: 35px; color: rgba(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="4402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4402

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4402" class="line" lang="c">       <span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">unistr_buffer_space</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">feature_name_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chro_name_pos_delta</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4335" style="width: 35px; color: rgba(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="4403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4403

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4403" class="line" lang="c">       <span class="n" style="color: #333;">loaded_features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">is_negative_strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">?</span><span class="sc" style="color: #d14;">'N'</span><span class="o" style="font-weight: 600;">:</span><span class="p">(</span>  <span class="n" style="color: #333;">loaded_features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">is_negative_strand</span> <span class="o" style="font-weight: 600;">==</span>  <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'P'</span><span class="o" style="font-weight: 600;">:</span><span class="sc" style="color: #d14;">'X'</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4335" style="width: 35px; color: rgba(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="4404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4404

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4404" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4335

</td>

<td class="diff-line-num new_line" data-linenumber="4405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4405

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4405" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4336" 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">

4336

</td>

<td class="diff-line-num new_line old" data-linenumber="4406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4336" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">xkk</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;">xkk</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">used_cell_barcode_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">xkk</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4337" 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">

4337

</td>

<td class="diff-line-num new_line old" data-linenumber="4406" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4337" class="line" lang="c">                   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">cell_bcno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcode_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">xkk</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4338" 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">

4338

</td>

<td class="diff-line-num new_line old" data-linenumber="4406" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4338" 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;">cell_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_cell_barcodes_array</span><span class="p">,</span> <span class="n" style="color: #333;">cell_bcno</span> <span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4339" 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">

4339

</td>

<td class="diff-line-num new_line old" data-linenumber="4406" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4339" class="line" lang="c">                   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s.%s"</span><span class="p">,</span> <span class="n" style="color: #333;">cell_name</span><span class="p">,</span> <span class="n" style="color: #333;">sample_name</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4406

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4406" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_write_sparse_matrix</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_tab_gene_to_cell_umis</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cell_barcode_tab</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">used_cell_barcodes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample_index</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tabtype</span><span class="p">,</span> <span class="n" style="color: #333;">fc_feature_info_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4407

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4407" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span><span class="n" style="color: #333;">x2</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4408

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4408" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4409

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4409" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ofname</span><span class="p">[</span><span class="n" style="color: #333;">MAX_FILE_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">100</span><span class="p">];</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4410

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4410" class="line" lang="c">   <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofname</span><span class="p">,</span><span class="s" style="color: #d14;">"%s.scRNA.%03d.%s.BCtab"</span><span class="p">,</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">sample_index</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;">tabtype</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4411

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4411" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ofp_bcs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span> <span class="n" style="color: #333;">ofname</span> <span class="p">,</span> <span class="s" style="color: #d14;">"w"</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4412

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4412" class="line" lang="c">   <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofname</span><span class="p">,</span><span class="s" style="color: #d14;">"%s.scRNA.%03d.%s.GENEtab"</span><span class="p">,</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">sample_index</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;">tabtype</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4413

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4413" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ofp_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span> <span class="n" style="color: #333;">ofname</span> <span class="p">,</span> <span class="s" style="color: #d14;">"w"</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4414

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4414" class="line" lang="c">   <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofname</span><span class="p">,</span><span class="s" style="color: #d14;">"%s.scRNA.%03d.%s.spmtx"</span><span class="p">,</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">sample_index</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;">tabtype</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4415

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4415" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ofp_mtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span> <span class="n" style="color: #333;">ofname</span> <span class="p">,</span> <span class="s" style="color: #d14;">"w"</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4416

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4416" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp_mtx</span><span class="p">,</span><span class="s" style="color: #d14;">"%%%%MatrixMarket matrix coordinate integer general</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4417

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4417" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4418

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4418" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">used_cell_barcodes_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListToLookupTable_Int</span><span class="p">(</span> <span class="n" style="color: #333;">used_cell_barcodes</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4419

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4419" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4420

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4420" class="line" lang="c">   <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output_gene_idxs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableKeys</span><span class="p">(</span><span class="n" style="color: #333;">merged_tab_gene_to_cell_umis</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4421

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4421" class="line" lang="c">   <span class="n" style="color: #333;">ArrayListSort</span><span class="p">(</span><span class="n" style="color: #333;">output_gene_idxs</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4422

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4422" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nonzero_items</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;">nonozero_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4423

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4423" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bc_no_to_output_no_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableCreate</span><span class="p">(</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_cell_barcodes_array</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">8</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4424

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4424" class="line" lang="c">   <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output_no_tab_to_bcno_arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListCreate</span><span class="p">(</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_cell_barcodes_array</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4425

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4425" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">output_gene_idxs</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4426

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4426" class="line" lang="c">           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">gene_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">output_gene_idxs</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4427

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4427" class="line" lang="c">           <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bc_umi_p1_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">merged_tab_gene_to_cell_umis</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gene_index</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4428

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4428" class="line" lang="c">           <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">bc_umi_p1_list</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4429

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4429" class="line" lang="c">           <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">bc_umi_p1_list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4430

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4430" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4431

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4431" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">old_bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">this_gene_has_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4432

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<pre style="margin: 0;">+<span id="LC4432" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x2</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;">x2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bc_umi_p1_list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4433

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<pre style="margin: 0;">+<span id="LC4433" class="line" lang="c">                   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">bc_umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">bc_umi_p1_list</span><span class="p">,</span> <span class="n" style="color: #333;">x2</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4434

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<pre style="margin: 0;">+<span id="LC4434" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">bc_umi</span> <span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">32</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4435

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<pre style="margin: 0;">+<span id="LC4435" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">this_bc_needed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcodes_tab</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bc_no</span><span class="p">);</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4436

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4436" 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;">this_bc_needed</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4437

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<pre style="margin: 0;">+<span id="LC4437" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">out_bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span> <span class="n" style="color: #333;">bc_no_to_output_no_tab</span> <span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bc_no</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>

</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="4340" style="width: 35px; color: rgba(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="4438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4438

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4438" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">out_bc_no</span> <span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span> <span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4439

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4439" class="line" lang="c">                           <span class="n" style="color: #333;">out_bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc_no_to_output_no_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4440

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<pre style="margin: 0;">+<span id="LC4440" class="line" lang="c">                           <span class="n" style="color: #333;">HashTablePut</span><span class="p">(</span>  <span class="n" style="color: #333;">bc_no_to_output_no_tab</span> <span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bc_no</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_bc_no</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4441

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4441" class="line" lang="c">                           <span class="n" style="color: #333;">ArrayListPush</span><span class="p">(</span><span class="n" style="color: #333;">output_no_tab_to_bcno_arr</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bc_no</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4442

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4442" class="line" lang="c">                           <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp_bcs</span><span class="p">,</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="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;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_cell_barcodes_array</span><span class="p">,</span> <span class="n" style="color: #333;">bc_no</span><span class="p">));</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4443

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4443" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4444

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4444" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4445

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<pre style="margin: 0;">+<span id="LC4445" class="line" lang="c">                   <span class="n" style="color: #333;">this_gene_has_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4446

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4446" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">old_bc_no</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bc_no</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4447

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4447" class="line" lang="c">                           <span class="n" style="color: #333;">nonzero_items</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4448

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4448" class="line" lang="c">                           <span class="n" style="color: #333;">old_bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc_no</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4449

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4449" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4450

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4450" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4451

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4451" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">this_gene_has_bc</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4340" style="width: 35px; color: rgba(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="4452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4452

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4452" class="line" lang="c">                   <span class="n" style="color: #333;">nonozero_genes</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4340

</td>

<td class="diff-line-num new_line" data-linenumber="4453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4453

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4453" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4341" 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">

4341

</td>

<td class="diff-line-num new_line old" data-linenumber="4454" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4341" class="line" lang="c">           <span class="n" style="color: #333;">cell_items_row</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xkk</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4342

</td>

<td class="diff-line-num new_line" data-linenumber="4454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4454

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4454" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4343" 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">

4343

</td>

<td class="diff-line-num new_line old" data-linenumber="4455" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4343" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4344" 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">

4344

</td>

<td class="diff-line-num new_line old" data-linenumber="4455" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4344" class="line" lang="c"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4345" 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">

4345

</td>

<td class="diff-line-num new_line old" data-linenumber="4455" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4345" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">uniq_gene_nos_in_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableCreate</span><span class="p">(</span><span class="mi" style="color: #099;">10000</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4346" 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">

4346

</td>

<td class="diff-line-num new_line old" data-linenumber="4455" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4346" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_sample_sheet_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4347" 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">

4347

</td>

<td class="diff-line-num new_line old" data-linenumber="4455" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4347" class="line" lang="c">           <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">appendix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">global_context</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4348" 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">

4348

</td>

<td class="diff-line-num new_line old" data-linenumber="4455" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4348" class="line" lang="c">           <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">appendix2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uniq_gene_nos_in_samples</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4349" 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">

4349

</td>

<td class="diff-line-num new_line old" data-linenumber="4455" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4349" class="line" lang="c">           <span class="n" style="color: #333;">HashTableIteration</span><span class="p">(</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">scRNA_merge_write_copy_gene_nos</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4455

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4455" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp_mtx</span><span class="p">,</span> <span class="s" style="color: #d14;">"%u %u %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nonozero_genes</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">bc_no_to_output_no_tab</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="p">,</span> <span class="n" style="color: #333;">nonzero_items</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4456

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<pre style="margin: 0;">+<span id="LC4456" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4457

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<pre style="margin: 0;">+<span id="LC4457" class="line" lang="c">   <span class="n" style="color: #333;">nonozero_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4458

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<pre style="margin: 0;">+<span id="LC4458" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">output_gene_idxs</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4459

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<pre style="margin: 0;">+<span id="LC4459" class="line" lang="c">           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">gene_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">output_gene_idxs</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4460

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<pre style="margin: 0;">+<span id="LC4460" class="line" lang="c">           <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bc_umi_p1_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">merged_tab_gene_to_cell_umis</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gene_index</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4461

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<pre style="margin: 0;">+<span id="LC4461" class="line" lang="c">           <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">bc_umi_p1_list</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4462

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<pre style="margin: 0;">+<span id="LC4462" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4463

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<pre style="margin: 0;">+<span id="LC4463" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mybc_UMIs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4464

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<pre style="margin: 0;">+<span id="LC4464" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">old_bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">old_out_bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">this_gene_has_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4465

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<pre style="margin: 0;">+<span id="LC4465" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x2</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;">x2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bc_umi_p1_list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4466

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<pre style="margin: 0;">+<span id="LC4466" class="line" lang="c">                   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">bc_umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">bc_umi_p1_list</span><span class="p">,</span> <span class="n" style="color: #333;">x2</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4467

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<pre style="margin: 0;">+<span id="LC4467" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">bc_umi</span> <span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">32</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4468

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<pre style="margin: 0;">+<span id="LC4468" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">out_bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span> <span class="n" style="color: #333;">bc_no_to_output_no_tab</span> <span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bc_no</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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4469

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<pre style="margin: 0;">+<span id="LC4469" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">this_bc_needed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcodes_tab</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bc_no</span><span class="p">);</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4470

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<pre style="margin: 0;">+<span id="LC4470" 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;">this_bc_needed</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4471

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4471" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4472

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<pre style="margin: 0;">+<span id="LC4472" class="line" lang="c">                   <span class="n" style="color: #333;">this_gene_has_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4473

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4473" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">old_bc_no</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bc_no</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4474

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<pre style="margin: 0;">+<span id="LC4474" class="line" lang="c">                           <span class="n" style="color: #333;">mybc_UMIs</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4475

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<pre style="margin: 0;">+<span id="LC4475" class="line" lang="c">                   <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4476

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4476" class="line" lang="c">                           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">old_out_bc_no</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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp_mtx</span><span class="p">,</span><span class="s" style="color: #d14;">"%d %d %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nonozero_genes</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;">old_out_bc_no</span><span class="p">,</span> <span class="n" style="color: #333;">mybc_UMIs</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4477

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4477" class="line" lang="c">                           <span class="n" style="color: #333;">old_bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc_no</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4478

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4478" class="line" lang="c">                           <span class="n" style="color: #333;">old_out_bc_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_bc_no</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4479

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4479" class="line" lang="c">                           <span class="n" style="color: #333;">mybc_UMIs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4480

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4480" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4481

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4481" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4482

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4482" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mybc_UMIs</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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp_mtx</span><span class="p">,</span><span class="s" style="color: #d14;">"%d %d %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nonozero_genes</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;">old_out_bc_no</span><span class="p">,</span> <span class="n" style="color: #333;">mybc_UMIs</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4483

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4483" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4484

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4484" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">this_gene_has_bc</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4485

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4485" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_gene_level</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4486

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4486" 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;">gene_name</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;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">gene_name_array</span> <span class="p">[</span><span class="n" style="color: #333;">gene_index</span><span class="p">];</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4487

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4487" class="line" lang="c">                           <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp_genes</span><span class="p">,</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">gene_name</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4488

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4488" class="line" lang="c">                   <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4489

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4489" class="line" lang="c">                           <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">exon_name</span><span class="p">[</span><span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">60</span><span class="p">];</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4490

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4490" class="line" lang="c">                           <span class="n" style="color: #333;">build_exon_name</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">,</span> <span class="n" style="color: #333;">gene_index</span><span class="p">,</span> <span class="n" style="color: #333;">exon_name</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4491

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4491" class="line" lang="c">                           <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp_genes</span><span class="p">,</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">exon_name</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4492

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4492" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4493

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4493" class="line" lang="c">                   <span class="c1" style="color: #998; font-style: italic;">//if(x1 < 7) SUBREADprintf("GOT A GENE SMP_%d: [%d]  %s\n", sample_index+1, x1, gene_name);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4494

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4494" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4350" style="width: 35px; color: rgba(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="4495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4495

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4495" class="line" lang="c">           <span class="n" style="color: #333;">nonozero_genes</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">this_gene_has_bc</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4350

</td>

<td class="diff-line-num new_line" data-linenumber="4496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4496

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4496" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4351" style="width: 35px; color: rgba(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="4497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4497

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4497" class="line" lang="c">   <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">bc_no_to_output_no_tab</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4351" style="width: 35px; color: rgba(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="4498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4498

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4498" class="line" lang="c">   <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcodes_tab</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4351" style="width: 35px; color: rgba(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="4499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4499

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4499" class="line" lang="c">   <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">output_gene_idxs</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4351" style="width: 35px; color: rgba(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="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4500

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4500" class="line" lang="c">   <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">ofp_bcs</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4351" style="width: 35px; color: rgba(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="4501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4501

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4501" class="line" lang="c">   <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">ofp_genes</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4351" style="width: 35px; color: rgba(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="4502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4502

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4502" class="line" lang="c">   <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">ofp_mtx</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4351

</td>

<td class="diff-line-num new_line" data-linenumber="4503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4503

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4503" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4352" 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">

4352

</td>

<td class="diff-line-num new_line old" data-linenumber="4504" 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="LC4352" class="line" lang="c">   <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gen_no_list_raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableKeys</span><span class="p">(</span><span class="n" style="color: #333;">uniq_gene_nos_in_samples</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4353" 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">

4353

</td>

<td class="diff-line-num new_line old" data-linenumber="4504" 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="LC4353" class="line" lang="c">   <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gen_no_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListCreate</span><span class="p">(</span><span class="n" style="color: #333;">gen_no_list_raw</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4354" 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">

4354

</td>

<td class="diff-line-num new_line old" data-linenumber="4504" 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="LC4354" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">gen_no_list_raw</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="p">;</span><span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4355" 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">

4355

</td>

<td class="diff-line-num new_line old" data-linenumber="4504" 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="LC4355" class="line" lang="c">           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">gene_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">gen_no_list_raw</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4356" 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">

4356

</td>

<td class="diff-line-num new_line old" data-linenumber="4504" 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="LC4356" class="line" lang="c">           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">UMIs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span> <span class="n" style="color: #333;">uniq_gene_nos_in_samples</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gene_no</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4357" 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">

4357

</td>

<td class="diff-line-num new_line old" data-linenumber="4504" 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="LC4357" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">UMIs</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">MIN_EXPRESSED_UMIS_PER_GENE</span><span class="p">)</span> <span class="n" style="color: #333;">ArrayListPush</span><span class="p">(</span> <span class="n" style="color: #333;">gen_no_list</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gene_no</span> <span class="p">);</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4504

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4504" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4505

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4505" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4506

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4506" class="line" lang="c"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4507

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4507" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_45K_to_90K_sum_SUM</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;">kyGeneID</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;">Vcb_umi_arr</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">me</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4508

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4508" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gene_to_umis</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">me</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4509

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4509" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bcid_look_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">me</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix2</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4510

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4510" class="line" lang="c">   <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cb_umi_arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Vcb_umi_arr</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4511

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4511" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4512

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4512" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="n" style="color: #333;">this_gene_added</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableGet</span><span class="p">(</span><span class="n" style="color: #333;">gene_to_umis</span><span class="p">,</span> <span class="n" style="color: #333;">kyGeneID</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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4513

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4513" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">has_adding</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4514

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4514" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cb_umi_arr</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4515

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4515" class="line" lang="c">           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">cb_umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">cb_umi_arr</span><span class="p">,</span><span class="n" style="color: #333;">x1</span><span class="p">)</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4516

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4516" class="line" lang="c">           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">cbno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cb_umi</span> <span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">32</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4517

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4517" 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;">HashTableGet</span><span class="p">(</span> <span class="n" style="color: #333;">bcid_look_tab</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">cbno</span> <span class="p">))</span><span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4518

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4518" class="line" lang="c">           <span class="n" style="color: #333;">this_gene_added</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4519

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4519" class="line" lang="c">           <span class="n" style="color: #333;">has_adding</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4520

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4520" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4521

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4521" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">has_adding</span><span class="p">)</span><span class="n" style="color: #333;">HashTablePut</span><span class="p">(</span><span class="n" style="color: #333;">gene_to_umis</span><span class="p">,</span> <span class="n" style="color: #333;">kyGeneID</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">this_gene_added</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4522

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4522" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4523

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4523" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4524

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4524" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_45K_to_90K_sum_WRT</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;">kyGeneID</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;">valUMIs</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">me</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4525

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4525" class="line" lang="c">   <span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">me</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4526

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4526" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ofp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">me</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix2</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4527

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4527" class="line" lang="c">   <span class="n" style="color: #333;">fc_feature_info_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">loaded_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">me</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">appendix3</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4528

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4528" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4529

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4529" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_gene_level</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4530

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4530" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gene_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">gene_name_array</span><span class="p">[</span> <span class="n" style="color: #333;">kyGeneID</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="mi" style="color: #099;">1</span> <span class="p">];</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4531

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4531" class="line" lang="c">           <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">gene_name</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">valUMIs</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">));</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4532

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4532" class="line" lang="c">   <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4533

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4533" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">exon_name</span><span class="p">[</span><span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">60</span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4534

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4534" class="line" lang="c">           <span class="n" style="color: #333;">build_exon_name</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">,</span> <span class="n" style="color: #333;">kyGeneID</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">exon_name</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4358" style="width: 35px; color: rgba(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="4535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4535

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4535" class="line" lang="c">           <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp</span><span class="p">,</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">exon_name</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">valUMIs</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">));</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4358

</td>

<td class="diff-line-num new_line" data-linenumber="4536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4536

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4536" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4359" 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">

4359

</td>

<td class="diff-line-num new_line old" data-linenumber="4537" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4359" class="line" lang="c">   <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">gen_no_list_raw</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4360" 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">

4360

</td>

<td class="diff-line-num new_line old" data-linenumber="4537" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4360" class="line" lang="c">   <span class="n" style="color: #333;">ArrayListSort</span><span class="p">(</span><span class="n" style="color: #333;">gen_no_list</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4361" style="width: 35px; color: rgba(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="4537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4537

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4537" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4361

</td>

<td class="diff-line-num new_line" data-linenumber="4538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4538

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4538" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4362" 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">

4362

</td>

<td class="diff-line-num new_line old" data-linenumber="4539" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4362" 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;">linebuf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cell_items_row</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">MAX_GENE_NAME_LEN</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">6</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4363" 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">

4363

</td>

<td class="diff-line-num new_line old" data-linenumber="4539" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4363" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">xkk</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;">xkk</span> <span class="o" style="font-weight: 600;"><</span>  <span class="n" style="color: #333;">gen_no_list</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span><span class="p">;</span> <span class="n" style="color: #333;">xkk</span> <span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4364" 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">

4364

</td>

<td class="diff-line-num new_line old" data-linenumber="4539" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4364" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">should_write</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scRNA_merged_write_a_gene</span><span class="p">(</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">,</span> <span class="n" style="color: #333;">used_cell_barcode_tabs</span><span class="p">,</span> <span class="n" style="color: #333;">used_cell_barcode_list</span><span class="p">,</span> <span class="n" style="color: #333;">merged_umi_list</span><span class="p">,</span> <span class="n" style="color: #333;">gen_no_list</span><span class="p">,</span> <span class="n" style="color: #333;">xkk</span><span class="p">,</span>  <span class="n" style="color: #333;">linebuf</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4365" 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">

4365

</td>

<td class="diff-line-num new_line old" data-linenumber="4539" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4365" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">should_write</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4366" 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">

4366

</td>

<td class="diff-line-num new_line old" data-linenumber="4539" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4366" class="line" lang="c">                   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofp</span><span class="p">,</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">linebuf</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4539

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4539" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_45K_to_90K_sum</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gene_to_cell_umis_tab</span><span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bcid_arr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample_no</span><span class="p">,</span> <span class="n" style="color: #333;">fc_feature_info_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">loaded_features</span> <span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4540

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4540" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashTableCreate</span><span class="p">(</span> <span class="n" style="color: #333;">gene_to_cell_umis_tab</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOfElements</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">6</span> <span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4541

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4541" class="line" lang="c">   <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bcid_look_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListToLookupTable_Int</span><span class="p">(</span><span class="n" style="color: #333;">bcid_arr</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4542

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4542" class="line" lang="c">   <span class="n" style="color: #333;">gene_to_cell_umis_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4543

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4543" class="line" lang="c">   <span class="n" style="color: #333;">gene_to_cell_umis_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcid_look_tab</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4544

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4544" class="line" lang="c">   <span class="n" style="color: #333;">HashTableIteration</span><span class="p">(</span> <span class="n" style="color: #333;">gene_to_cell_umis_tab</span><span class="p">,</span> <span class="n" style="color: #333;">scRNA_merged_45K_to_90K_sum_SUM</span> <span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4545

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4545" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4546

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4546" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ofname</span><span class="p">[</span><span class="n" style="color: #333;">MAX_FILE_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">100</span><span class="p">];</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4547

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4547" class="line" lang="c">   <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofname</span><span class="p">,</span><span class="s" style="color: #d14;">"%s.scRNA.%03d.AmbSum"</span><span class="p">,</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">sample_no</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4548

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4548" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">write_fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">ofname</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4549

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4549" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">write_fp</span><span class="p">,</span><span class="s" style="color: #d14;">"GeneID</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">UMIs</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4550

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4550" class="line" lang="c">   <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">global_context</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4551

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4551" class="line" lang="c">   <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_fp</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4552

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4552" class="line" lang="c">   <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4553

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4553" class="line" lang="c">   <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">counter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_no</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4554

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4554" class="line" lang="c">   <span class="n" style="color: #333;">HashTableIteration</span><span class="p">(</span> <span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">scRNA_merged_45K_to_90K_sum_WRT</span> <span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4555

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4555" class="line" lang="c">   <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">bcid_look_tab</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4556

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4556" class="line" lang="c">   <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4557

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4557" class="line" lang="c">   <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">write_fp</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4367" style="width: 35px; color: rgba(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="4558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4558

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4558" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4367

</td>

<td class="diff-line-num new_line" data-linenumber="4559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4559

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4559" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4560

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4560" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_write_nozero_geneids_WRT</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;">k</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;">v</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">me</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4561

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4561" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">me</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">appendix1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4562

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4562" class="line" lang="c">   <span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">me</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">appendix2</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4563

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4563" class="line" lang="c">   <span class="n" style="color: #333;">fc_feature_info_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">loaded_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">me</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">appendix3</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4564

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4564" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_gene_level</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4565

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4565" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gene_symbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">gene_name_array</span> <span class="p">[</span><span class="n" style="color: #333;">k</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="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4566

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4566" 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;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">gene_symbol</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4567

</td>

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<pre style="margin: 0;">+<span id="LC4567" class="line" lang="c">   <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4568

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4568" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">exon_name</span><span class="p">[</span><span class="n" style="color: #333;">FEATURE_NAME_LENGTH</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">60</span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4569

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4569" class="line" lang="c">           <span class="n" style="color: #333;">build_exon_name</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">,</span> <span class="n" style="color: #333;">k</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">exon_name</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4368" style="width: 35px; color: rgba(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="4570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4570

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4570" 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;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">exon_name</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4368

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<td class="diff-line-num new_line" data-linenumber="4571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4571

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4571" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4369" 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">

4369

</td>

<td class="diff-line-num new_line old" data-linenumber="4572" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4369" class="line" lang="c"><span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">free</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">linebuf</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4370" style="width: 35px; color: rgba(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="4572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4572

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<pre style="margin: 0;">+<span id="LC4572" class="line" lang="c"><span class="p"><span class="idiff left right">}</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4370

</td>

<td class="diff-line-num new_line" data-linenumber="4573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4573

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4573" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4371" 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">

4371

</td>

<td class="diff-line-num new_line old" data-linenumber="4574" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4371" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_sample_sheet_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4372" 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">

4372

</td>

<td class="diff-line-num new_line old" data-linenumber="4574" 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="LC4372" class="line" lang="c">           <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcode_list</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">]);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4373" 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">

4373

</td>

<td class="diff-line-num new_line old" data-linenumber="4574" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4373" class="line" lang="c">   <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">used_cell_barcode_list</span><span class="p">);</span> </span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4374" style="width: 35px; color: rgba(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="4574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4574

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4574" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_write_nozero_geneids</span><span class="p">(</span>  <span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gene_to_cell_umis_tab</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">samplenno</span><span class="p">,</span> <span class="n" style="color: #333;">fc_feature_info_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">loaded_features</span> <span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4374" style="width: 35px; color: rgba(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="4575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4575

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4575" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ofname</span><span class="p">[</span><span class="n" style="color: #333;">MAX_FILE_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">100</span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4374" style="width: 35px; color: rgba(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="4576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4576

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4576" class="line" lang="c">   <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofname</span><span class="p">,</span><span class="s" style="color: #d14;">"%s.scRNA.%03d.no0Genes"</span><span class="p">,</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">samplenno</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4374" style="width: 35px; color: rgba(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="4577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4577

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4577" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span> <span class="n" style="color: #333;">ofname</span> <span class="p">,</span> <span class="s" style="color: #d14;">"w"</span> <span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4374" style="width: 35px; color: rgba(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="4578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4578

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4578" class="line" lang="c">   <span class="n" style="color: #333;">gene_to_cell_umis_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix1</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fp</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4374" style="width: 35px; color: rgba(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="4579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4579

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<pre style="margin: 0;">+<span id="LC4579" class="line" lang="c">   <span class="n" style="color: #333;">gene_to_cell_umis_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix2</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">global_context</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4374" style="width: 35px; color: rgba(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="4580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4580

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<pre style="margin: 0;">+<span id="LC4580" class="line" lang="c">   <span class="n" style="color: #333;">gene_to_cell_umis_tab</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">appendix3</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loaded_features</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4374" style="width: 35px; color: rgba(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="4581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4581

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4581" class="line" lang="c">   <span class="n" style="color: #333;">HashTableIteration</span><span class="p">(</span><span class="n" style="color: #333;">gene_to_cell_umis_tab</span><span class="p">,</span> <span class="n" style="color: #333;">scRNA_merged_write_nozero_geneids_WRT</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4374" style="width: 35px; color: rgba(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="4582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4582

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4582" class="line" lang="c">   <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4374" style="width: 35px; color: rgba(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="4583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4583

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4583" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4374

</td>

<td class="diff-line-num new_line" data-linenumber="4584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4584

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4584" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4375" 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">

4375

</td>

<td class="diff-line-num new_line old" data-linenumber="4585" 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="LC4375" class="line" lang="c">   <span class="n" style="color: #333;">HashTableDestroy</span><span class="p">(</span><span class="n" style="color: #333;">uniq_gene_nos_in_samples</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4376" 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">

4376

</td>

<td class="diff-line-num new_line old" data-linenumber="4585" 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="LC4376" class="line" lang="c">   <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">gen_no_list</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4377" 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">

4377

</td>

<td class="diff-line-num new_line old" data-linenumber="4585" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4377" class="line" lang="c">   <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">ofp</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4585

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<pre style="margin: 0;">+<span id="LC4585" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// this function writes a single count table.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4586

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<pre style="margin: 0;">+<span id="LC4586" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Rows: genes</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4587

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<pre style="margin: 0;">+<span id="LC4587" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Cols: Cell_Barcode +"."+ SampleName</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4588

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4588" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scRNA_merged_to_tables_write</span><span class="p">(</span> <span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span> <span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">used_cell_barcode_tabs</span> <span class="p">,</span> <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_umi_list</span><span class="p">,</span> <span class="n" style="color: #333;">fc_feature_info_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4589

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4589" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ofname</span><span class="p">[</span><span class="n" style="color: #333;">MAX_FILE_NAME_LENGTH</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">20</span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4590

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<pre style="margin: 0;">+<span id="LC4590" class="line" lang="c">   <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">ofname</span><span class="p">,</span><span class="s" style="color: #d14;">"%s.scRNA.SampleTable"</span><span class="p">,</span><span class="n" style="color: #333;">global_context</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input_file_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4591

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4591" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_tab_fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span> <span class="n" style="color: #333;">ofname</span> <span class="p">,</span> <span class="s" style="color: #d14;">"w"</span> <span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4592

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4592" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4593

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4593" class="line" lang="c"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4594

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<pre style="margin: 0;">+<span id="LC4594" class="line" lang="c">   <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">sample_tab_fp</span><span class="p">,</span><span class="s" style="color: #d14;">"SampleName</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Index</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4595

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<pre style="margin: 0;">+<span id="LC4595" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">x1</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;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_sample_sheet_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">numOfElements</span> <span class="p">;</span> <span class="n" style="color: #333;">x1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4596

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4596" 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;">this_sample_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListGet</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">scRNA_sample_id_to_name</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4597

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4597" class="line" lang="c">           <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">sample_tab_fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">this_sample_name</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4598

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<pre style="margin: 0;">+<span id="LC4598" class="line" lang="c">           <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">high_confid_barcode_index_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListCreate</span><span class="p">(</span><span class="mi" style="color: #099;">20000</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4599

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4599" class="line" lang="c">           <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">this_sample_ambient_rescure_candi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListCreate</span><span class="p">(</span><span class="mi" style="color: #099;">10000</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4600

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<pre style="margin: 0;">+<span id="LC4600" class="line" lang="c">           <span class="n" style="color: #333;">ArrayList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">this_sample_45k_90k_barcode_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArrayListCreate</span><span class="p">(</span><span class="mi" style="color: #099;">90000</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">45000</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">100</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4601

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4601" class="line" lang="c">           <span class="n" style="color: #333;">scRNA_merged_bootstrap_a_sample</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">used_cell_barcode_tabs</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span><span class="n" style="color: #333;">merged_umi_list</span><span class="p">,</span> <span class="n" style="color: #333;">high_confid_barcode_index_list</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4602

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4602" class="line" lang="c">           <span class="n" style="color: #333;">scRNA_merged_ambient_rescure</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">used_cell_barcode_tabs</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">this_sample_ambient_rescure_candi</span><span class="p">,</span> <span class="n" style="color: #333;">this_sample_45k_90k_barcode_idx</span><span class="p">,</span> <span class="n" style="color: #333;">high_confid_barcode_index_list</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4603

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4603" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4604

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4604" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("HAVING_HIGHCONF_TOTAL %lld\n", high_confid_barcode_index_list -> numOfElements);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4605

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4605" class="line" lang="c">           <span class="n" style="color: #333;">scRNA_merged_write_sparse_matrix</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">used_cell_barcode_tabs</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">high_confid_barcode_index_list</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="s" style="color: #d14;">"HighConf"</span><span class="p">,</span>  <span class="n" style="color: #333;">loaded_features</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4606

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4606" class="line" lang="c">           <span class="n" style="color: #333;">scRNA_merged_write_sparse_matrix</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">used_cell_barcode_tabs</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">this_sample_ambient_rescure_candi</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="s" style="color: #d14;">"RescCand"</span><span class="p">,</span>  <span class="n" style="color: #333;">loaded_features</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4607

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4607" class="line" lang="c">           <span class="n" style="color: #333;">scRNA_merged_45K_to_90K_sum</span><span class="p">(</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">this_sample_45k_90k_barcode_idx</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span> <span class="p">,</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4608

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<pre style="margin: 0;">+<span id="LC4608" class="line" lang="c">           <span class="n" style="color: #333;">scRNA_merged_write_nozero_geneids</span><span class="p">(</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">merged_tables_gene_to_cell_umis</span><span class="p">[</span><span class="n" style="color: #333;">x1</span><span class="p">],</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="n" style="color: #333;">loaded_features</span> <span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4609

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4609" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4610

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<pre style="margin: 0;">+<span id="LC4610" class="line" lang="c">           <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">this_sample_ambient_rescure_candi</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4611

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<pre style="margin: 0;">+<span id="LC4611" class="line" lang="c">           <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">this_sample_45k_90k_barcode_idx</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4612

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4612" class="line" lang="c">           <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">high_confid_barcode_index_list</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4613

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<pre style="margin: 0;">+<span id="LC4613" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4614

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4614" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4378" style="width: 35px; color: rgba(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="4615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4615

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<pre style="margin: 0;">+<span id="LC4615" class="line" lang="c">   <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">sample_tab_fp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4378

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<td class="diff-line-num new_line" data-linenumber="4616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4616

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<pre style="margin: 0;"> <span id="LC4616" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4379

</td>

<td class="diff-line-num new_line" data-linenumber="4617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4617

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4617" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4380

</td>

<td class="diff-line-num new_line" data-linenumber="4618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4618

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<pre style="margin: 0;"> <span id="LC4618" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span>  <span class="nf" style="color: #900; font-weight: 600;">scRNA_merge_merge_UMIs</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;">gno_ky</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;">cell_umi_2_reads_list_va</span> <span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tab</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4389" style="width: 35px; color: rgba(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="4627" style="width: 35px; color: rgba(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">@@ -4389,7 +4627,7 @@ void  scRNA_merge_merge_UMIs(void * gno_ky, void * cell_umi_2_reads_list_va , Ha</td>

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<td class="diff-line-num old_line" data-linenumber="4389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4389

</td>

<td class="diff-line-num new_line" data-linenumber="4627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4627

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<pre style="margin: 0;"> <span id="LC4627" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4390

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<td class="diff-line-num new_line" data-linenumber="4628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4628

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4628" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4391

</td>

<td class="diff-line-num new_line" data-linenumber="4629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4629

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<pre style="margin: 0;"> <span id="LC4629" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// return the number of RG result sets</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4392" 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">

4392

</td>

<td class="diff-line-num new_line old" data-linenumber="4630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4392" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">fc_thread_merge_results</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">read_count_type_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nreads</span> <span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nreads_mapped_to_exon</span><span class="p">,</span> <span class="n" style="color: #333;">fc_read_counters</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">my_read_counter</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">junction_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">splicing_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">RGmerged_table</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4393" style="width: 35px; color: rgba(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="4630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4630

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<pre style="margin: 0;">+<span id="LC4630" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">fc_thread_merge_results</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">read_count_type_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nreads</span> <span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nreads_mapped_to_exon</span><span class="p">,</span> <span class="n" style="color: #333;">fc_read_counters</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">my_read_counter</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">junction_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">splicing_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">RGmerged_table</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fc_feature_info_t</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">loaded_features</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4393

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<td class="diff-line-num new_line" data-linenumber="4631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4631

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<pre style="margin: 0;"> <span id="LC4631" class="line" lang="c"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4394

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<td class="diff-line-num new_line" data-linenumber="4632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4632

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<pre style="margin: 0;"> <span id="LC4632" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xk1</span><span class="p">,</span> <span class="n" style="color: #333;">xk2</span><span class="p">,</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4395

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<td class="diff-line-num new_line" data-linenumber="4633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4633

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4633" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4442" style="width: 35px; color: rgba(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="4680" style="width: 35px; color: rgba(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">@@ -4442,7 +4680,7 @@ int fc_thread_merge_results(fc_thread_global_context_t * global_context, read_co</td>

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<td class="diff-line-num old_line" data-linenumber="4442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4442

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<td class="diff-line-num new_line" data-linenumber="4680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4680

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<pre style="margin: 0;"> <span id="LC4680" class="line" lang="c">                   <span class="n" style="color: #333;">HashTableIteration</span><span class="p">(</span>  <span class="n" style="color: #333;">merged_sample_cell_umi_tables</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">],</span> <span class="n" style="color: #333;">scRNA_merge_merge_UMIs</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4443

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<td class="diff-line-num new_line" data-linenumber="4681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4681

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<pre style="margin: 0;"> <span id="LC4681" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4444

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<td class="diff-line-num new_line" data-linenumber="4682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4682

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<pre style="margin: 0;"> <span id="LC4682" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4445" 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">

4445

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<td class="diff-line-num new_line old" data-linenumber="4683" 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="LC4445" class="line" lang="c">           <span class="n" style="color: #333;">scRNA_merged_to_tables_write</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="p">,</span> <span class="n" style="color: #333;">merged_sample_cell_umi_tables</span> <span class="p">,</span> <span class="n" style="color: #333;">used_cell_no_tables</span><span class="p">,</span> <span class="n" style="color: #333;">merged_umi_list</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4446" style="width: 35px; color: rgba(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="4683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4683

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<pre style="margin: 0;">+<span id="LC4683" class="line" lang="c">           <span class="n" style="color: #333;">scRNA_merged_to_tables_write</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="p">,</span> <span class="n" style="color: #333;">merged_sample_cell_umi_tables</span> <span class="p">,</span> <span class="n" style="color: #333;">used_cell_no_tables</span><span class="p">,</span> <span class="n" style="color: #333;">merged_umi_list</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">loaded_features</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4446

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<td class="diff-line-num new_line" data-linenumber="4684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4684

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<pre style="margin: 0;"> <span id="LC4684" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4447

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<td class="diff-line-num new_line" data-linenumber="4685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4685

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<pre style="margin: 0;"> <span id="LC4685" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//  SUBREADprintf("MERGED UMI TABLE = %ld items\n", merged_umi_table -> numOfElements);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4448

</td>

<td class="diff-line-num new_line" data-linenumber="4686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4686

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<pre style="margin: 0;"> <span id="LC4686" class="line" lang="c">           <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">merged_umi_list</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5629" style="width: 35px; color: rgba(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="5867" style="width: 35px; color: rgba(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">@@ -5629,9 +5867,11 @@ void print_usage()</td>

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<td class="diff-line-num old_line" data-linenumber="5629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5629

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<td class="diff-line-num new_line" data-linenumber="5867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5867

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<pre style="margin: 0;"> <span id="LC5867" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"                      'SAF'. 'GTF' by default.  For SAF format, please refer to"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5630

</td>

<td class="diff-line-num new_line" data-linenumber="5868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5868

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5868" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"                      Users Guide."</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5631

</td>

<td class="diff-line-num new_line" data-linenumber="5869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5869

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5869" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="5632" 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">

5632

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<td class="diff-line-num new_line old" data-linenumber="5870" 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="LC5632" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"  -t <string>         Specify feature type in GTF annotation. 'exon' by "</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="5633" 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">

5633

</td>

<td class="diff-line-num new_line old" data-linenumber="5870" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5633" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"                      default. Features used for read counting will be "</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="5634" 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">

5634

</td>

<td class="diff-line-num new_line old" data-linenumber="5870" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5634" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"                      extracted from annotation using the provided value."</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5635" style="width: 35px; color: rgba(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="5870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5870

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5870" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"  -t <string>         Specify feature type(s) in a GTF annotation. If multiple"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="5635" style="width: 35px; color: rgba(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="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5871

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5871" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"                      types are provided, they should be separated by ',' with"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5635" style="width: 35px; color: rgba(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="5872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5872

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5872" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"                      no space in between. 'exon' by default. Rows in the"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="5635" style="width: 35px; color: rgba(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="5873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5873

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5873" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"                      annotation with a matched feature will be extracted and"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="5635" style="width: 35px; color: rgba(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="5874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5874

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5874" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"                      used for read mapping. "</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="5635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5635

</td>

<td class="diff-line-num new_line" data-linenumber="5875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5875

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<pre style="margin: 0;"> <span id="LC5875" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5636

</td>

<td class="diff-line-num new_line" data-linenumber="5876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5876

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5876" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"  -g <string>         Specify attribute type in GTF annotation. 'gene_id' by "</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5637

</td>

<td class="diff-line-num new_line" data-linenumber="5877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5877

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5877" class="line" lang="c">   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"                      default. Meta-features used for read counting will be "</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6206" style="width: 35px; color: rgba(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="6446" style="width: 35px; color: rgba(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">@@ -6206,7 +6446,7 @@ HashTable * scRNA_copy_loaded_features(srInt_64 nexons, fc_feature_info_t* loade</td>

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<td class="diff-line-num old_line" data-linenumber="6206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6206

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<td class="diff-line-num new_line" data-linenumber="6446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6446

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<pre style="margin: 0;"> <span id="LC6446" class="line" lang="c">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6207

</td>

<td class="diff-line-num new_line" data-linenumber="6447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6447

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<pre style="margin: 0;"> <span id="LC6447" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6208

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<td class="diff-line-num new_line" data-linenumber="6448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6448

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6448" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6209" 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">

6209

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<td class="diff-line-num new_line old" data-linenumber="6449" 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="LC6209" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">readSummary_single_file</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">read_count_type_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">column_numbers</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">nexons</span><span class="p">,</span>  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">geneid</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sorted_strand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">anno_chr_2ch</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">anno_chrs</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">anno_chr_head</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_end_index</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_min_start</span> <span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_max_end</span><span class="p">,</span> <span class="n" style="color: #333;">fc_read_counters</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">my_read_counter</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">junc_glob_tab</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">splicing_glob_tab</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_RG_table</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6210" style="width: 35px; color: rgba(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="6449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6449

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<pre style="margin: 0;">+<span id="LC6449" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">readSummary_single_file</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">read_count_type_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">column_numbers</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">nexons</span><span class="p">,</span>  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">geneid</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sorted_strand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">anno_chr_2ch</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">anno_chrs</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">anno_chr_head</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_end_index</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_min_start</span> <span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_max_end</span><span class="p">,</span> <span class="n" style="color: #333;">fc_read_counters</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">my_read_counter</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">junc_glob_tab</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">splicing_glob_tab</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_RG_table</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fc_feature_info_t</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">loaded_features</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6210

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<td class="diff-line-num new_line" data-linenumber="6450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6450

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<pre style="margin: 0;"> <span id="LC6450" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6211

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<td class="diff-line-num new_line" data-linenumber="6451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6451

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<pre style="margin: 0;"> <span id="LC6451" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">Input_Files_And_Strand_Mode_Pair</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fnames</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">smodes</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6212

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<td class="diff-line-num new_line" data-linenumber="6452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6452

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<pre style="margin: 0;"> <span id="LC6452" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</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;">ch</span><span class="p">,</span> <span class="n" style="color: #333;">bad_fmt</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;">numbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6737" style="width: 35px; color: rgba(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="6977" style="width: 35px; color: rgba(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">@@ -6737,7 +6977,7 @@ int readSummary(int argc,char *argv[]){</td>

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<td class="diff-line-num old_line" data-linenumber="6737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6737

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<td class="diff-line-num new_line" data-linenumber="6977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6977

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<pre style="margin: 0;"> <span id="LC6977" class="line" lang="c">           <span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">is_read_details_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isReadSummaryReport</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6738

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<td class="diff-line-num new_line" data-linenumber="6978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6978

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<pre style="margin: 0;"> <span id="LC6978" class="line" lang="c">           <span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">max_M</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_M</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6739

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<td class="diff-line-num new_line" data-linenumber="6979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6979

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<pre style="margin: 0;"> <span id="LC6979" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6740" 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">

6740

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<td class="diff-line-num new_line old" data-linenumber="6980" 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="LC6740" class="line" lang="c">           <span class="n" style="color: #333;">ret_int</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ret_int</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">readSummary_single_file</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">column_numbers</span><span class="p">,</span> <span class="n" style="color: #333;">nexons</span><span class="p">,</span> <span class="n" style="color: #333;">geneid</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">sorted_strand</span><span class="p">,</span> <span class="n" style="color: #333;">anno_chr_2ch</span><span class="p">,</span> <span class="n" style="color: #333;">anno_chrs</span><span class="p">,</span> <span class="n" style="color: #333;">anno_chr_head</span><span class="p">,</span> <span class="n" style="color: #333;">block_end_index</span><span class="p">,</span> <span class="n" style="color: #333;">block_min_start</span><span class="p">,</span> <span class="n" style="color: #333;">block_max_end</span><span class="p">,</span> <span class="n" style="color: #333;">my_read_counter</span><span class="p">,</span> <span class="n" style="color: #333;">junction_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">splicing_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">merged_RG_table</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6741" style="width: 35px; color: rgba(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="6980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6980

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<pre style="margin: 0;">+<span id="LC6980" class="line" lang="c">           <span class="n" style="color: #333;">ret_int</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ret_int</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">readSummary_single_file</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">column_numbers</span><span class="p">,</span> <span class="n" style="color: #333;">nexons</span><span class="p">,</span> <span class="n" style="color: #333;">geneid</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">sorted_strand</span><span class="p">,</span> <span class="n" style="color: #333;">anno_chr_2ch</span><span class="p">,</span> <span class="n" style="color: #333;">anno_chrs</span><span class="p">,</span> <span class="n" style="color: #333;">anno_chr_head</span><span class="p">,</span> <span class="n" style="color: #333;">block_end_index</span><span class="p">,</span> <span class="n" style="color: #333;">block_min_start</span><span class="p">,</span> <span class="n" style="color: #333;">block_max_end</span><span class="p">,</span> <span class="n" style="color: #333;">my_read_counter</span><span class="p">,</span> <span class="n" style="color: #333;">junction_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">splicing_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">merged_RG_table</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">loaded_features</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6741

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<td class="diff-line-num new_line" data-linenumber="6981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6981

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<pre style="margin: 0;"> <span id="LC6981" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">disk_is_full</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6742

</td>

<td class="diff-line-num new_line" data-linenumber="6982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6982

</td>

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<pre style="margin: 0;"> <span id="LC6982" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: disk is full. Please check the free space in the output directory.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6743

</td>

<td class="diff-line-num new_line" data-linenumber="6983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6983

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6983" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6806" style="width: 35px; color: rgba(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="7046" style="width: 35px; color: rgba(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">@@ -6806,6 +7046,7 @@ int readSummary(int argc,char *argv[]){</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6806

</td>

<td class="diff-line-num new_line" data-linenumber="7046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7046

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7046" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">is_input_bad_format</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6807

</td>

<td class="diff-line-num new_line" data-linenumber="7047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7047

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7047" class="line" lang="c">           <span class="n" style="color: #333;">SUBREADprintf</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;">FATAL Error: The program has to terminate and no counting file is generated.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6808

</td>

<td class="diff-line-num new_line" data-linenumber="7048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7048

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7048" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">disk_is_full</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6809" style="width: 35px; color: rgba(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="7049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7049

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7049" class="line" lang="c">           <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Write the final count table."</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6809

</td>

<td class="diff-line-num new_line" data-linenumber="7050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7050

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7050" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isGeneLevel</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6810

</td>

<td class="diff-line-num new_line" data-linenumber="7051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7051

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7051" 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;">sorted_extra_columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6811

</td>

<td class="diff-line-num new_line" data-linenumber="7052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7052

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7052" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">reported_extra_columns</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6823" style="width: 35px; color: rgba(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="7064" style="width: 35px; color: rgba(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">@@ -6823,11 +7064,15 @@ int readSummary(int argc,char *argv[]){</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6823

</td>

<td class="diff-line-num new_line" data-linenumber="7064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7064

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7064" class="line" lang="c">           <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6824

</td>

<td class="diff-line-num new_line" data-linenumber="7065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7065

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7065" class="line" lang="c">                   <span class="n" style="color: #333;">fc_write_final_results</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">nexons</span><span class="p">,</span> <span class="n" style="color: #333;">table_columns</span><span class="p">,</span> <span class="n" style="color: #333;">table_column_names</span><span class="p">,</span> <span class="n" style="color: #333;">loaded_features</span><span class="p">,</span> <span class="n" style="color: #333;">isCVersion</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6825

</td>

<td class="diff-line-num new_line" data-linenumber="7066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7066

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7066" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="6826" 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">

6826

</td>

<td class="diff-line-num new_line old" data-linenumber="7067" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6826" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">do_junction_counting</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">disk_is_full</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6827" style="width: 35px; color: rgba(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="7067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7067

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7067" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">do_junction_counting</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">is_input_bad_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">disk_is_full</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6827" style="width: 35px; color: rgba(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="7068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7068

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7068" class="line" lang="c">           <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Write the junction count table."</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6827

</td>

<td class="diff-line-num new_line" data-linenumber="7069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7069

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7069" class="line" lang="c">           <span class="n" style="color: #333;">fc_write_final_junctions</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">table_column_names</span><span class="p">,</span> <span class="n" style="color: #333;">junction_global_table_list</span><span class="p">,</span> <span class="n" style="color: #333;">splicing_global_table_list</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6828" style="width: 35px; color: rgba(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="7070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7070

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7070" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6828

</td>

<td class="diff-line-num new_line" data-linenumber="7071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7071

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7071" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="6829" 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">

6829

</td>

<td class="diff-line-num new_line old" data-linenumber="7072" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6829" 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;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">disk_is_full</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6830" style="width: 35px; color: rgba(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="7072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7072

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7072" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">is_input_bad_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">global_context</span><span class="p">.</span><span class="n" style="color: #333;">disk_is_full</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6830" style="width: 35px; color: rgba(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="7073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7073

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7073" class="line" lang="c">           <span class="n" style="color: #333;">print_in_box</span><span class="p">(</span><span class="mi" style="color: #099;">80</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"Write the read assignment summary."</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6830

</td>

<td class="diff-line-num new_line" data-linenumber="7074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7074

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7074" class="line" lang="c">           <span class="n" style="color: #333;">fc_write_final_counts</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">table_column_names</span><span class="p">,</span>  <span class="n" style="color: #333;">read_counters</span><span class="p">,</span> <span class="n" style="color: #333;">isCVersion</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6831" style="width: 35px; color: rgba(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="7075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7075

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7075" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6831

</td>

<td class="diff-line-num new_line" data-linenumber="7076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7076

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7076" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6832

</td>

<td class="diff-line-num new_line" data-linenumber="7077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7077

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7077" class="line" lang="c">   <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">table_columns</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6833

</td>

<td class="diff-line-num new_line" data-linenumber="7078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7078

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7078" class="line" lang="c">   <span class="n" style="color: #333;">ArrayListDestroy</span><span class="p">(</span><span class="n" style="color: #333;">table_column_names</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6962" style="width: 35px; color: rgba(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="7207" style="width: 35px; color: rgba(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">@@ -6962,7 +7207,7 @@ void sort_bucket_table(fc_thread_global_context_t * global_context){</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6962

</td>

<td class="diff-line-num new_line" data-linenumber="7207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7207

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7207" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6963

</td>

<td class="diff-line-num new_line" data-linenumber="7208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7208

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7208" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6964

</td>

<td class="diff-line-num new_line" data-linenumber="7209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7209

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7209" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="6965" 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">

6965

</td>

<td class="diff-line-num new_line old" data-linenumber="7210" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6965" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">readSummary_single_file</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">read_count_type_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">column_numbers</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">nexons</span><span class="p">,</span>  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">geneid</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sorted_strand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">anno_chr_2ch</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">anno_chrs</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">anno_chr_head</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_end_index</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_min_start</span> <span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_max_end</span><span class="p">,</span> <span class="n" style="color: #333;">fc_read_counters</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">my_read_counter</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">junction_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">splicing_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_RG_table</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6966" style="width: 35px; color: rgba(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="7210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7210

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<pre style="margin: 0;">+<span id="LC7210" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">readSummary_single_file</span><span class="p">(</span><span class="n" style="color: #333;">fc_thread_global_context_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">read_count_type_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">column_numbers</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">nexons</span><span class="p">,</span>  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">geneid</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sorted_strand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">anno_chr_2ch</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">anno_chrs</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">anno_chr_head</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_end_index</span><span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_min_start</span> <span class="p">,</span> <span class="n" style="color: #333;">srInt_64</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">block_max_end</span><span class="p">,</span> <span class="n" style="color: #333;">fc_read_counters</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">my_read_counter</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">junction_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">splicing_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_RG_table</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fc_feature_info_t</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">loaded_features</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6966

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<td class="diff-line-num new_line" data-linenumber="7211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7211

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<pre style="margin: 0;"> <span id="LC7211" class="line" lang="c"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6967

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<td class="diff-line-num new_line" data-linenumber="7212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7212

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<pre style="margin: 0;"> <span id="LC7212" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">read_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6968

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<td class="diff-line-num new_line" data-linenumber="7213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7213

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<pre style="margin: 0;"> <span id="LC7213" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">is_first_read_PE</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7000" style="width: 35px; color: rgba(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="7245" style="width: 35px; color: rgba(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">@@ -7000,7 +7245,7 @@ int readSummary_single_file(fc_thread_global_context_t * global_context, read_co</td>

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<td class="diff-line-num old_line" data-linenumber="7000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7000

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<td class="diff-line-num new_line" data-linenumber="7245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7245

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<pre style="margin: 0;"> <span id="LC7245" class="line" lang="c">   <span class="n" style="color: #333;">fc_thread_wait_threads</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7001

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<td class="diff-line-num new_line" data-linenumber="7246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7246

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<pre style="margin: 0;"> <span id="LC7246" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7002

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<td class="diff-line-num new_line" data-linenumber="7247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7247

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<pre style="margin: 0;"> <span id="LC7247" class="line" lang="c">   <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">nreads_mapped_to_exon</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7003" 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">

7003

</td>

<td class="diff-line-num new_line old" data-linenumber="7248" 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="LC7003" class="line" lang="c">   <span class="n" style="color: #333;">fc_thread_merge_results</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">column_numbers</span> <span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nreads_mapped_to_exon</span><span class="p">,</span> <span class="n" style="color: #333;">my_read_counter</span><span class="p">,</span> <span class="n" style="color: #333;">junction_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">splicing_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">merged_RG_table</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7004" style="width: 35px; color: rgba(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="7248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7248

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<pre style="margin: 0;">+<span id="LC7248" class="line" lang="c">   <span class="n" style="color: #333;">fc_thread_merge_results</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">,</span> <span class="n" style="color: #333;">column_numbers</span> <span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nreads_mapped_to_exon</span><span class="p">,</span> <span class="n" style="color: #333;">my_read_counter</span><span class="p">,</span> <span class="n" style="color: #333;">junction_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">splicing_global_table</span><span class="p">,</span> <span class="n" style="color: #333;">merged_RG_table</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">loaded_features</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7004

</td>

<td class="diff-line-num new_line" data-linenumber="7249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7249

</td>

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<pre style="margin: 0;"> <span id="LC7249" class="line" lang="c">   <span class="n" style="color: #333;">fc_thread_destroy_thread_context</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7005

</td>

<td class="diff-line-num new_line" data-linenumber="7250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7250

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7250" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7006

</td>

<td class="diff-line-num new_line" data-linenumber="7251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7251

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7251" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">sambam_chro_table</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">global_context</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">sambam_chro_table</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7031" style="width: 35px; color: rgba(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="7276" style="width: 35px; color: rgba(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">@@ -7031,7 +7276,7 @@ int feature_count_main(int argc, char ** argv)</td>

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<td class="diff-line-num old_line" data-linenumber="7031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7031

</td>

<td class="diff-line-num new_line" data-linenumber="7276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7276

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<pre style="margin: 0;"> <span id="LC7276" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cmd_rebuilt_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2000</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7032

</td>

<td class="diff-line-num new_line" data-linenumber="7277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7277

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7277" 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;">cmd_rebuilt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">cmd_rebuilt_size</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7033

</td>

<td class="diff-line-num new_line" data-linenumber="7278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7278

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7278" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">max_M_str</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="7034" 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">

7034

</td>

<td class="diff-line-num new_line old" data-linenumber="7279" 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="LC7034" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nameFeatureTypeColumn</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">66</span></span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="7035" style="width: 35px; color: rgba(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="7279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7279

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7279" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nameFeatureTypeColumn</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">2000</span></span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7035

</td>

<td class="diff-line-num new_line" data-linenumber="7280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7280

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7280" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nameGeneIDColumn</span><span class="p">[</span><span class="mi" style="color: #099;">66</span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7036

</td>

<td class="diff-line-num new_line" data-linenumber="7281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7281

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7281" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_qual_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7037

</td>

<td class="diff-line-num new_line" data-linenumber="7282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7282

</td>

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<pre style="margin: 0;"> <span id="LC7282" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="f86ff9b8aeda4b6603bb5a33b2b3a6251be1c2e9">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#f86ff9b8aeda4b6603bb5a33b2b3a6251be1c2e9"><strong>src/sambam-file.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -557,7 +557,8 @@ int PBam_chunk_headers(char * chunk, int *chunk_ptr, int chunk_len, SamBam_Refer</td>

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<td class="diff-line-num 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">

557

</td>

<td class="diff-line-num new_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">

557

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c">                                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

558

</td>

<td class="diff-line-num new_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

558

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC558" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

559

</td>

<td class="diff-line-num new_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

559

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<pre style="margin: 0;"> <span id="LC559" class="line" lang="c">                                    <span class="n" style="color: #333;">SamBam_Reference_Info</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_event</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;">bam_chro_table</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;">table_items</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="560" 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">

560

</td>

<td class="diff-line-num new_line old" data-linenumber="560" 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="LC560" class="line" lang="c">                                    <span class="n" style="color: #333;">strncpy</span><span class="p">(</span><span class="n" style="color: #333;">new_event</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chro_name</span><span class="p">,</span> <span class="n" style="color: #333;">chro_name</span><span class="p">,</span> <span class="n" style="color: #333;">BAM_MAX_CHROMOSOME_NAME_LEN</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">chro_name</span><span class="p">)</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">BAM_MAX_CHROMOSOME_NAME_LEN</span><span class="p">)</span> <span class="n" style="color: #333;">chro_name</span><span class="p">[</span><span class="n" style="color: #333;">BAM_MAX_CHROMOSOME_NAME_LEN</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">new_event</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chro_name</span><span class="p">,</span> <span class="n" style="color: #333;">chro_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

561

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<td class="diff-line-num new_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

562

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<pre style="margin: 0;"> <span id="LC562" class="line" lang="c">                                    <span class="n" style="color: #333;">new_event</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">chro_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chro_len</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

562

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<td class="diff-line-num new_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

563

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<pre style="margin: 0;"> <span id="LC563" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

563

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<td class="diff-line-num new_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

564

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="c">                                    <span class="p">(</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_items</span><span class="p">)</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1782" style="width: 35px; color: rgba(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="1783" style="width: 35px; color: rgba(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">@@ -1782,7 +1783,7 @@ int SamBam_unzip(char * out , char * in , int inlen)</td>

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1782

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<td class="diff-line-num new_line" data-linenumber="1783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1783

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<pre style="margin: 0;"> <span id="LC1783" class="line" lang="c"><span class="p">}</span></span>

</pre>

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1783

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<td class="diff-line-num new_line" data-linenumber="1784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1784

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<pre style="margin: 0;"> <span id="LC1784" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1784

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<td class="diff-line-num new_line" data-linenumber="1785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1785

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<pre style="margin: 0;"> <span id="LC1785" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1785" 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">

1785

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<td class="diff-line-num new_line old" data-linenumber="1786" 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="LC1785" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">SamBam_writer_sort_buff_one_compare</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;">Lbin</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;">Rbin</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1786" style="width: 35px; color: rgba(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="1786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1786

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<pre style="margin: 0;">+<span id="LC1786" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">SamBam_writer_sort_buff_one_compare</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;">Lbin</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;">Rbin</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">me</span></span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1786

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<td class="diff-line-num new_line" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1787

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<pre style="margin: 0;"> <span id="LC1787" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Lv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Lbin</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Rv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Rbin</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1787

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<td class="diff-line-num new_line" data-linenumber="1788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1788

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<pre style="margin: 0;"> <span id="LC1788" 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;">Lv</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Rv</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1788

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<td class="diff-line-num new_line" data-linenumber="1789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1789

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<pre style="margin: 0;"> <span id="LC1789" class="line" lang="c">   <span class="k" style="font-weight: 600;">else</span> <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;">Lv</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Rv</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2052" style="width: 35px; color: rgba(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="2053" style="width: 35px; color: rgba(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">@@ -2052,7 +2053,7 @@ void SamBam_writer_one_thread_merge_sortedbins(SamBam_Writer * writer){</td>

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<td class="diff-line-num old_line" data-linenumber="2052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2052

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<td class="diff-line-num new_line" data-linenumber="2053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2053

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2053" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2053

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<td class="diff-line-num new_line" data-linenumber="2054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2054

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<pre style="margin: 0;"> <span id="LC2054" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">level_min_binno</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">73</span><span class="p">,</span> <span class="mi" style="color: #099;">585</span><span class="p">,</span> <span class="mi" style="color: #099;">4681</span><span class="p">};</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2055" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="2056" 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="LC2055" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">SamBam_writer_merge_chunks_compare</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;">vL</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;">vR</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2056" style="width: 35px; color: rgba(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="2056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2056" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">SamBam_writer_merge_chunks_compare</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;">vL</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;">vR</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">me</span></span><span class="p">){</span></span>

</pre>

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2056

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<td class="diff-line-num new_line" data-linenumber="2057" style="width: 35px; color: rgba(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="LC2057" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2058" style="width: 35px; color: rgba(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="LC2058" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vR</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC2059" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lL</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;">lR</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="03fc71344ae0dba380c866ea91a52d0334a86e42">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#03fc71344ae0dba380c866ea91a52d0334a86e42"><strong>src/sorted-hashtable.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" style="width: 35px; color: rgba(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="125" style="width: 35px; color: rgba(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">@@ -125,9 +125,9 @@ int _gehash_resize_bucket(gehash_t * the_table , int bucket_no, char is_small_ta</td>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">is_small_table</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="128" 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="LC128" class="line" lang="c">                    <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">GEHASH_BUCKET_LENGTH</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c">                    <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">5</span></span><span class="idiff right"> </span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(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="LC129" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="130" 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="LC130" class="line" lang="c">                    <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">GEHASH_BUCKET_LENGTH</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" style="width: 35px; color: rgba(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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c">                    <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="idiff right"> </span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(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="LC133" class="line" lang="c">                    <span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -167,7 +167,7 @@ int _gehash_resize_bucket(gehash_t * the_table , int bucket_no, char is_small_ta</td>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c">                    <span class="c1" style="color: #998; font-style: italic;">//new_bucket_length = (int)max(15,current_bucket->space_size*1.5+1);</span></span>

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<td class="diff-line-num old_line" data-linenumber="168" style="width: 35px; color: rgba(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="LC168" class="line" lang="c">                    <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">5</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="169" style="width: 35px; color: rgba(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="LC169" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span></span>

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<td class="diff-line-num old old_line" data-linenumber="170" 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="LC170" class="line" lang="c">                    <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">current_bucket</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">space_size</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="p"><span class="idiff right">);</span></span></span>

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<td class="diff-line-num new old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c">                    <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">max</span></span><span class="p"><span class="idiff">((</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">current_bucket</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">space_size</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">current_bucket</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">space_size</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="p"><span class="idiff">));</span></span><span class="idiff right">    </span></span>

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<td class="diff-line-num old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="171" style="width: 35px; color: rgba(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="LC171" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="172" style="width: 35px; color: rgba(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="LC172" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="173" style="width: 35px; color: rgba(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="LC173" class="line" lang="c">                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">realloc</span><span class="p">(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span> <span class="p">,</span>  <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="188" style="width: 35px; color: rgba(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="188" style="width: 35px; color: rgba(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">@@ -188,200 +188,6 @@ int _gehash_resize_bucket(gehash_t * the_table , int bucket_no, char is_small_ta</td>

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<td class="diff-line-num old_line" data-linenumber="188" style="width: 35px; color: rgba(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="LC188" 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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<pre style="margin: 0;"> <span id="LC189" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="c"></span>

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<td class="diff-line-num old old_line" data-linenumber="191" 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="LC191" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">_gehash_resize_bucket_old</span><span class="p">(</span><span class="n" style="color: #333;">gehash_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">the_table</span> <span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bucket_no</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">is_small_table</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="192" 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">

192

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC192" class="line" lang="c"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="193" 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">

193

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC193" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="194" 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">

194

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC194" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">gehash_bucket</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span> <span class="p">[</span><span class="n" style="color: #333;">bucket_no</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="195" 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">

195

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC195" class="line" lang="c">    <span class="n" style="color: #333;">gehash_key_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="196" 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">

196

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC196" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="197" 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">

197

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC197" class="line" lang="c">    <span class="n" style="color: #333;">gehash_data_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_item_values</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="198" 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">

198

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC198" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="199" 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">

199

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC199" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="200" 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">

200

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC200" class="line" lang="c">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

201

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">randv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myrand_rand</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

202

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">is_small_table</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="203" 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">

203

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC203" class="line" lang="c">                    <span class="c1" style="color: #998; font-style: italic;">//new_bucket_length = (int)max(15,current_bucket->space_size*1.5+1);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="204" 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">

204

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC204" class="line" lang="c">                    <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">GEHASH_BUCKET_LENGTH</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">.</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">randv</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">RAND_MAX</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">)));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="205" 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">

205

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC205" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="206" 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">

206

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC206" class="line" lang="c">                    <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">GEHASH_BUCKET_LENGTH</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">.</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">.</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">randv</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">RAND_MAX</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">)));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="207" 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">

207

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC207" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC208" class="line" lang="c"></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  printf("NS1=%d\nNS2=%d\n", new_bucket_length, new_bucket_length);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC210" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC211" class="line" lang="c">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC212" class="line" lang="c">                    <span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="213" 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="LC213" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="214" 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="LC214" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC215" class="line" lang="c">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC216" class="line" lang="c">                    <span class="n" style="color: #333;">new_new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="217" 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="LC217" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="218" 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="LC218" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC219" class="line" lang="c">            <span class="n" style="color: #333;">new_item_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC220" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="221" 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="LC221" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">((</span><span class="n" style="color: #333;">new_item_keys</span><span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">new_new_item_keys</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">new_item_values</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="222" 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="LC222" class="line" lang="c">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC223" class="line" lang="c">                    <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="n" style="color: #333;">MESSAGE_OUT_OF_MEMORY</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC224" class="line" lang="c">                    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC225" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC227" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="228" 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">

228

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC228" class="line" lang="c">                    <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">new_item_keys</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="229" 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">

229

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC229" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="230" 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">

230

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC230" class="line" lang="c">                    <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">new_new_item_keys</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="231" 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">

231

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC231" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="232" 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">

232

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC232" class="line" lang="c">            <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">new_item_values</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="233" 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">

233

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC233" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="234" 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">

234

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC234" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></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="235" 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">

235

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC235" class="line" lang="c">                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_item_keys</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="236" 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">

236

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC236" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="237" 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">

237

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC237" class="line" lang="c">                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_new_item_keys</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="238" 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">

238

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC238" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="239" 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">

239

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC239" class="line" lang="c">            <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_item_values</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="240" 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">

240

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC240" class="line" lang="c">            <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="241" 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">

241

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC241" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="242" 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">

242

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC242" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="243" 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">

243

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC243" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

244

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC244" class="line" lang="c">    <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC245" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">test_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myrand_rand</span><span class="p">()</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC246" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC247" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">need_allowc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="248" 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">

248

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC248" 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="n" style="color: #333;">test_start</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">test_start</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10000</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC249" class="line" lang="c">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="250" 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="LC250" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">bucket_no</span><span class="p">)</span><span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="251" 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="LC251" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="252" 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="LC252" class="line" lang="c">                    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="253" 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="LC253" class="line" lang="c">                            <span class="n" style="color: #333;">test_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myrand_rand</span><span class="p">()</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="254" 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="LC254" class="line" lang="c">                            <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">test_start</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="255" 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="LC255" class="line" lang="c">                            <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="256" 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="LC256" class="line" lang="c">                    <span class="p">}</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC258" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">space_size</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_items</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">current_items</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_items</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">current_items</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC259" class="line" lang="c">                    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="260" 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="LC260" class="line" lang="c">                            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="261" 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="LC261" class="line" lang="c">                            <span class="n" style="color: #333;">gehash_data_t</span> <span class="n" style="color: #333;">t_d</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="262" 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="LC262" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC263" class="line" lang="c">                            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_items</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC264" class="line" lang="c">                            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC265" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">current_items</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="266" 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">

266

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c">                                    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC267" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="268" 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="LC268" class="line" lang="c">                                            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC269" class="line" lang="c">                                                    <span class="n" style="color: #333;">gehash_key_t</span> <span class="n" style="color: #333;">t_key</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="270" 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="LC270" class="line" lang="c">                                                    <span class="n" style="color: #333;">t_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="271" 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="LC271" class="line" lang="c">                                                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="272" 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="LC272" class="line" lang="c">                                                    <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_key</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC273" class="line" lang="c">                                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC274" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC275" class="line" lang="c">                                            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC276" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC277" class="line" lang="c">                                                    <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">t_key</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC278" class="line" lang="c">                                                    <span class="n" style="color: #333;">t_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">new_item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="c">                                                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">new_item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">new_item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="c">                                                    <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">new_item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_key</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC281" class="line" lang="c">                                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="282" 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="LC282" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="283" 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="LC283" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="284" 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="LC284" class="line" lang="c">                                            <span class="n" style="color: #333;">t_d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_values</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

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<td class="diff-line-num old old_line" data-linenumber="285" 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="LC285" class="line" lang="c">                                            <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_values</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">item_values</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="c">                                            <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">item_values</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_d</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="c">                                    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="c">                                    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="290" 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="LC290" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="291" 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="LC291" class="line" lang="c">                                                    <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC292" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="293" 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="LC293" class="line" lang="c">                                                    <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">new_item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">new_item_keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="294" 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="LC294" class="line" lang="c">                                            <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">item_values</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_values</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="295" 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="LC295" class="line" lang="c">                                    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC297" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="298" 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="LC298" class="line" lang="c">                            <span class="n" style="color: #333;">gehash_key_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p_key</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC299" class="line" lang="c">                            <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ps_key</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="300" 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="LC300" class="line" lang="c">                            <span class="n" style="color: #333;">gehash_data_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p_d</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="301" 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="LC301" class="line" lang="c">                            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i_size</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="302" 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="LC302" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="303" 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="LC303" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="304" 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="LC304" class="line" lang="c">                            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="305" 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="LC305" class="line" lang="c">                                    <span class="n" style="color: #333;">p_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">item_keys</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="306" 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="LC306" class="line" lang="c">                                    <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="307" 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="LC307" class="line" lang="c">                                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p_key</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="308" 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="LC308" class="line" lang="c">                            <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="309" 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="LC309" class="line" lang="c">                                    <span class="n" style="color: #333;">ps_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">new_item_keys</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="c">                                    <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">new_item_keys</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="c">                                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ps_key</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="312" 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="LC312" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="313" 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="LC313" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="314" 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">

314

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC314" class="line" lang="c">                            <span class="n" style="color: #333;">p_d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">item_values</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="315" 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">

315

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC315" class="line" lang="c">                            <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">item_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_values</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="316" 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">

316

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC316" class="line" lang="c">                            <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p_d</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="317" 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">

317

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC317" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

318

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC318" class="line" lang="c">                            <span class="n" style="color: #333;">i_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">space_size</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="319" 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">

319

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC319" class="line" lang="c">                            <span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">space_size</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="320" 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">

320

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC320" class="line" lang="c">                            <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i_size</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

321

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="c">                            </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC322" class="line" lang="c">                            <span class="n" style="color: #333;">need_allowc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC323" class="line" lang="c">                            <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="324" 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">

324

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC324" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC325" class="line" lang="c">            <span class="p">}</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="326" 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">

326

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC326" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">need_allowc</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC327" class="line" lang="c">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

328

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">is_small_table</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="329" 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">

329

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<td class="diff-line-num new_line old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="c">                            <span class="c1" style="color: #998; font-style: italic;">//new_bucket_length = (int)max(15,current_bucket->space_size*1.5+1);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="330" 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">

330

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC330" class="line" lang="c">                            <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">5</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC331" class="line" lang="c">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="c">                            <span class="n" style="color: #333;">new_bucket_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">);</span></span>

</pre>

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333

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC333" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="334" 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="LC334" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//          printf("NSS1=%d\nNSS2=%d\n", new_bucket_length, new_bucket_length);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC335" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC336" class="line" lang="c">                            <span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="337" 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="LC337" class="line" lang="c">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="338" 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="LC338" class="line" lang="c">                            <span class="n" style="color: #333;">new_new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="339" 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="LC339" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="340" 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="LC340" class="line" lang="c">                    <span class="n" style="color: #333;">new_item_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC341" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="342" 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="LC342" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="343" 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="LC343" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">((</span><span class="n" style="color: #333;">new_item_keys</span><span class="o" style="font-weight: 600;">||</span><span class="n" style="color: #333;">new_new_item_keys</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">new_item_values</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="344" 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="LC344" class="line" lang="c">                    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC345" class="line" lang="c">                            <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="n" style="color: #333;">MESSAGE_OUT_OF_MEMORY</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="346" 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="LC346" class="line" lang="c">                            <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC347" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC348" class="line" lang="c"></span>

</pre>

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</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC349" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="350" 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">

350

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC350" class="line" lang="c">                            <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">new_item_keys</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="351" 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">

351

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC351" class="line" lang="c">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="352" 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">

352

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC352" class="line" lang="c">                            <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">new_new_item_keys</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="353" 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">

353

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC353" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="354" 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">

354

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC354" class="line" lang="c">                    <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">new_item_values</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="355" 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">

355

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC355" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="356" 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">

356

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC356" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="357" 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">

357

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC357" class="line" lang="c">                            <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">new_item_keys</span><span class="p">,</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span><span class="p">,</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_items</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_key_t</span><span class="p">));</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="358" 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">

358

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC358" class="line" lang="c">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="359" 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">

359

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC359" class="line" lang="c">                            <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">new_new_item_keys</span><span class="p">,</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span><span class="p">,</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_items</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;">short</span><span class="p">));</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="360" 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">

360

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC360" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

361

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC361" class="line" lang="c">                    <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">new_item_values</span><span class="p">,</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_values</span><span class="p">,</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_items</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">));</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="362" 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">

362

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC362" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="363" 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">

363

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC363" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="364" 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">

364

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC364" class="line" lang="c">                            <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="365" 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">

365

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC365" class="line" lang="c">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="366" 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">

366

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<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC366" class="line" lang="c">                            <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">new_item_keys</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="367" 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">

367

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC367" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="368" 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">

368

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC368" class="line" lang="c">                    <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_values</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="369" 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">

369

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC369" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="370" 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">

370

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC370" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">version_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SUBINDEX_VER0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="371" 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">

371

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC371" class="line" lang="c">                            <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_item_keys</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="372" 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">

372

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC372" class="line" lang="c">                    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="373" 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">

373

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC373" class="line" lang="c">                            <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_new_item_keys</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="374" 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">

374

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC374" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="375" 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">

375

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC375" class="line" lang="c">                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_item_values</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="376" 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">

376

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC376" class="line" lang="c">                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_bucket_length</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="377" 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">

377

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC377" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="378" 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">

378

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC378" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="379" 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">

379

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC379" class="line" lang="c">            <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="380" 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">

380

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC380" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="381" 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">

381

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC381" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="382" 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">

382

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC382" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="383" 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">

383

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC383" class="line" lang="c"><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="384" 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">

384

</td>

<td class="diff-line-num new_line old" data-linenumber="191" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC384" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

385

</td>

<td class="diff-line-num new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

191

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC191" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _gehash_get_bucket(tab, key)  ( (tab) -> buckets + _gehash_hash( key ) % (tab) -> buckets_number )</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _gehash_get_bucketNO(tab, key)  ( _gehash_hash( key ) % (tab) -> buckets_number )</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="419" style="width: 35px; color: rgba(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="225" style="width: 35px; color: rgba(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">@@ -419,13 +225,59 @@ int gehash_insert(gehash_t * the_table, gehash_key_t key, gehash_data_t data, un</td>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">step_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">new_item_keys</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;">bucket_sizes</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC422" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bkno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_gehash_get_bucketNO</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mem_block</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">((</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bucket_sizes</span><span class="p">[</span> <span class="n" style="color: #333;">bkno</span> <span class="p">]</span> <span class="p">);</span> </span>

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<pre style="margin: 0;">-<span id="LC424" class="line" lang="c">                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="n" style="color: #333;">gehash_data_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">)</span><span class="n" style="color: #333;">mem_block</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC425" class="line" lang="c">                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">short</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">mem_block</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span>  <span class="n" style="color: #333;">bucket_sizes</span><span class="p">[</span> <span class="n" style="color: #333;">bkno</span> <span class="p">])</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;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_items</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC427" class="line" lang="c">                    <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bucket_sizes</span><span class="p">[</span> <span class="n" style="color: #333;">bkno</span> <span class="p">];</span></span>

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<pre style="margin: 0;">-<span id="LC428" class="line" lang="c">                    <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">free_item_only</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="c">                    <span class="c1" style="color: #998; font-style: italic;">//this will go only once when all the bucktes are NULL.</span></span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">memory_sizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="c">                    <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">memory_sizes</span><span class="p">,</span> <span class="mh" style="color: #099;">0xff</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">grp_bytes</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;">grps</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;">this_grp_bucks</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;">xk1</span><span class="p">,</span> <span class="n" style="color: #333;">bucks_per_grp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">GEHASH_MEM_PTR_NO</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="c">                    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">xk1</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;">xk1</span><span class="o" style="font-weight: 600;"><</span>  <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span> <span class="p">;</span> <span class="n" style="color: #333;">xk1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="c">                            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">buck_size</span> <span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bucket_sizes</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="c">                            <span class="n" style="color: #333;">grp_bytes</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">buck_size</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="c">                            <span class="n" style="color: #333;">this_grp_bucks</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span>  <span class="n" style="color: #333;">this_grp_bucks</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">bucks_per_grp</span> <span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="c">                                    <span class="n" style="color: #333;">memory_sizes</span><span class="p">[</span><span class="n" style="color: #333;">grps</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;">grp_bytes</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="c">                                    <span class="n" style="color: #333;">grp_bytes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="c">                                    <span class="n" style="color: #333;">this_grp_bucks</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">this_grp_bucks</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c">                            <span class="n" style="color: #333;">memory_sizes</span><span class="p">[</span><span class="n" style="color: #333;">grps</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">grp_bytes</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="c">                    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">xk1</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;">xk1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">GEHASH_MEM_PTR_NO</span><span class="p">;</span> <span class="n" style="color: #333;">xk1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="c">                            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memory_sizes</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">current_bytes</span><span class="o" style="font-weight: 600;"><</span><span class="mh" style="color: #099;">0xff000000u</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">xk1</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>

</pre>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="c">                                            <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR : no-NULL ptr : %p</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">]);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="c">                                    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="c">                                    <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">current_bytes</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">]){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="c">                                            <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="n" style="color: #333;">MESSAGE_OUT_OF_MEMORY</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="c">                                    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="c">                    <span class="n" style="color: #333;">grp_bytes</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;">grps</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;">this_grp_bucks</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="c">                    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">xk1</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;">xk1</span><span class="o" style="font-weight: 600;"><</span>  <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span> <span class="p">;</span> <span class="n" style="color: #333;">xk1</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="c">                            <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">gehash_bucket</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mem_bucket</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">xk1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="c">                            <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">mem_bucket</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">gehash_bucket</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="c">                            <span class="n" style="color: #333;">mem_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="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;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">grps</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">grp_bytes</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c">                            <span class="n" style="color: #333;">mem_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">item_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</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;">mem_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">new_item_keys</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;">short</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bucket_sizes</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">]);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="c">                            <span class="n" style="color: #333;">mem_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">space_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bucket_sizes</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="c">                            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">buck_size</span> <span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bucket_sizes</span><span class="p">[</span><span class="n" style="color: #333;">xk1</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="c">                            <span class="n" style="color: #333;">grp_bytes</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">buck_size</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="c">                            <span class="n" style="color: #333;">this_grp_bucks</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span>  <span class="n" style="color: #333;">this_grp_bucks</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">bucks_per_grp</span> <span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="c">                                    <span class="n" style="color: #333;">grps</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="c">                                    <span class="n" style="color: #333;">grp_bytes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="c">                                    <span class="n" style="color: #333;">this_grp_bucks</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="c">                    <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">free_item_only</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="429" style="width: 35px; color: rgba(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="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

280

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="c">                    <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">memory_sizes</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

429

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<td class="diff-line-num new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

281

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

430

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<td class="diff-line-num new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

282

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

431

</td>

<td class="diff-line-num new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

283

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_items</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">current_bucket</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">space_size</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1548,7 +1400,7 @@ int gehash_load(gehash_t * the_table, const char fname [])</td>

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<td class="diff-line-num old_line" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1548

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<td class="diff-line-num new_line" data-linenumber="1400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1400

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<pre style="margin: 0;"> <span id="LC1400" class="line" lang="c">           <span class="c1" style="color: #998; font-style: italic;">//return -1;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1549

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<td class="diff-line-num new_line" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1401

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<pre style="margin: 0;"> <span id="LC1401" class="line" lang="c">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1550

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<td class="diff-line-num new_line" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1402

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<pre style="margin: 0;"> <span id="LC1402" class="line" lang="c">   </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1551" 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">

1551

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<td class="diff-line-num new_line old" data-linenumber="1403" 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="LC1551" class="line" lang="c">   <span class="n" style="color: #333;"><span class="idiff left">the_table</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">malloc_ptr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1552" style="width: 35px; color: rgba(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="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1403

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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="c">   <span class="n" style="color: #333;"><span class="idiff left">memset</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">the_table</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">malloc_ptr</span></span><span class="idiff"> </span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">GEHASH_MEM_PTR_NO</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1552

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<td class="diff-line-num new_line" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1404

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<pre style="margin: 0;"> <span id="LC1404" class="line" lang="c">   <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">index_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1553

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<td class="diff-line-num new_line" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1405

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1405" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1554

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<td class="diff-line-num new_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1406

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<pre style="margin: 0;"> <span id="LC1406" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f_subr_open</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1622" style="width: 35px; color: rgba(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="1474" style="width: 35px; color: rgba(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">@@ -1622,69 +1474,82 @@ int gehash_load(gehash_t * the_table, const char fname [])</td>

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<td class="diff-line-num old_line" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1622

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<td class="diff-line-num new_line" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1474

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<pre style="margin: 0;"> <span id="LC1474" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: the index format is unrecognizable."</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1623

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<td class="diff-line-num new_line" data-linenumber="1475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1475

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<pre style="margin: 0;"> <span id="LC1475" class="line" lang="c">                   <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span> <span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span> <span class="o" style="font-weight: 600;"><=</span><span class="mh" style="color: #099;">0xffffffffllu</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1624

</td>

<td class="diff-line-num new_line" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1476

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<pre style="margin: 0;"> <span id="LC1476" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1625" style="width: 35px; color: rgba(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="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1477

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1477" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1625" style="width: 35px; color: rgba(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="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1478

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1478" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bucket_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">GEHASH_MEM_PTR_NO</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1625" style="width: 35px; color: rgba(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="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1479

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1479" class="line" lang="c">           <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">bucket_bytes</span><span class="p">,</span> <span class="mh" style="color: #099;">0xff</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">GEHASH_MEM_PTR_NO</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1625

</td>

<td class="diff-line-num new_line" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1480

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1480" class="line" lang="c">           <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_int32</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1626

</td>

<td class="diff-line-num new_line" data-linenumber="1481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1481

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1481" class="line" lang="c">           <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">gehash_bucket</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">gehash_bucket</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1627

</td>

<td class="diff-line-num new_line" data-linenumber="1482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1482

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1482" 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;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1628

</td>

<td class="diff-line-num new_line" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1483

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1483" class="line" lang="c">           <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1629" style="width: 35px; color: rgba(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="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1484

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1484" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Creating buckets."</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1629

</td>

<td class="diff-line-num new_line" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1485

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1485" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="n" style="color: #333;">MESSAGE_OUT_OF_MEMORY</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1630

</td>

<td class="diff-line-num new_line" data-linenumber="1486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1486

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1486" class="line" lang="c">                   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1631

</td>

<td class="diff-line-num new_line" data-linenumber="1487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1487

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1487" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1632

</td>

<td class="diff-line-num new_line" data-linenumber="1488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1488

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1488" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1633" 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">

1633

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1633" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">fp_curr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftello</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">),</span> <span class="n" style="color: #333;">fp_end</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fp_curr</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1634" 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">

1634

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1634" class="line" lang="c">            </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1635" 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">

1635

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1635" class="line" lang="c">           <span class="n" style="color: #333;">fseeko</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_END</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1636" 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">

1636

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1636" class="line" lang="c">           <span class="n" style="color: #333;">fp_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftello</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span>     </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1637" 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">

1637

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1637" class="line" lang="c">           <span class="n" style="color: #333;">fseeko</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">fp_curr</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1638" 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">

1638

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1638" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//             SUBREADprintf("CACL_SIZE %zd %zd\n", fp_end, fp_curr);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1639" 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">

1639

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1639" class="line" lang="c">           </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1640" 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">

1640

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1640" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">rem_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fp_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">fp_curr</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1641" 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">

1641

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1641" class="line" lang="c">           <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">rem_len</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1642" 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">

1642

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1642" 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;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1643" 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">

1643

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1643" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="n" style="color: #333;">MESSAGE_OUT_OF_MEMORY</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1644" 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">

1644

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1644" class="line" lang="c">                   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1645" 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">

1645

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1645" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1646" 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">

1646

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1646" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1647" 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">

1647

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1647" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">rdbytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1648" 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">

1648

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1648" class="line" lang="c">           <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">feof</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;">rdbytes</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rem_len</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1649" 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">

1649

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1649" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">rrr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rdbytes</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">rem_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">rdbytes</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1650" 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">

1650

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1650" class="line" lang="c">                   <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("LOAD: %zd + %zd ==> %zd\n", rdbytes , rrr, rem_len);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1651" 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">

1651

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1651" class="line" lang="c">                   <span class="n" style="color: #333;">rdbytes</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rrr</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1652" 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">

1652

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1652" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1653" 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">

1653

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1653" class="line" lang="c">           <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1654" 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">

1654

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1654" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rdbytes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">rem_len</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1655" 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">

1655

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1655" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: the index cannot be fully loaded (%ld != %ld). It may contain format errors or file '%s' may be truncated.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span> <span class="n" style="color: #333;">fp_end</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span> <span class="n" style="color: #333;">fp_curr</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1656" 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">

1656

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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="LC1656" class="line" lang="c">                   <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1657" 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">

1657

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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="LC1657" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1658" 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">

1658

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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="LC1658" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rdbytes</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1659" 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">

1659

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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="LC1659" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: the index seem to contain no data at all. It may contain format errors or file '%s' may be truncated.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1660" 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">

1660

</td>

<td class="diff-line-num new_line old" data-linenumber="1489" 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="LC1660" class="line" lang="c">                   <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1489

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<pre style="margin: 0;">+<span id="LC1489" class="line" lang="c">           <span class="n" style="color: #333;">srInt_64</span> <span class="n" style="color: #333;">fp_curr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftello</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1490

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<pre style="margin: 0;">+<span id="LC1490" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">accued_bytes</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;">grp_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;">curr_bucks</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;">per_group_bucks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</span><span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">GEHASH_MEM_PTR_NO</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1491

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<pre style="margin: 0;">+<span id="LC1491" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1492

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<pre style="margin: 0;">+<span id="LC1492" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current_items</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_int32</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1493

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1493" class="line" lang="c">                   <span class="n" style="color: #333;">load_int32</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//useless for loading : space size</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1494

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1494" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_items</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">)</span> <span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1495

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1495" class="line" lang="c">                   <span class="n" style="color: #333;">accued_bytes</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">current_bytes</span><span class="p">;</span> </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1496

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1496" class="line" lang="c">                   <span class="n" style="color: #333;">curr_bucks</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1497

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1497" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">curr_bucks</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">per_group_bucks</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1498

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<pre style="margin: 0;">+<span id="LC1498" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("Allocating %d : %d buckets : %u\n", grp_i, i, accued_bytes);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1499

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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="c">                           <span class="n" style="color: #333;">bucket_bytes</span><span class="p">[</span><span class="n" style="color: #333;">grp_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;">accued_bytes</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1500

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<pre style="margin: 0;">+<span id="LC1500" class="line" lang="c">                           <span class="n" style="color: #333;">accued_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1501

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<pre style="margin: 0;">+<span id="LC1501" class="line" lang="c">                           <span class="n" style="color: #333;">curr_bucks</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1502

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1502" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1661" style="width: 35px; color: rgba(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="1503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1503

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<pre style="margin: 0;">+<span id="LC1503" class="line" lang="c">                   <span class="n" style="color: #333;">fseeko</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">current_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1661

</td>

<td class="diff-line-num new_line" data-linenumber="1504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1504

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<pre style="margin: 0;"> <span id="LC1504" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1662" 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">

1662

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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="LC1662" 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;">curr_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1663" 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">

1663

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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="LC1663" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1664" 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">

1664

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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="LC1664" class="line" lang="c">           <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1665" 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">

1665

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1665" class="line" lang="c">                   <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">gehash_bucket</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1666" 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">

1666

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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="LC1666" class="line" lang="c">                   <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span><span class="p">,</span> <span class="n" style="color: #333;">curr_ptr</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1667" 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">

1667

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1667" class="line" lang="c">                   <span class="n" style="color: #333;">curr_ptr</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1668" 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">

1668

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1668" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1669" 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">

1669

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1669" class="line" lang="c">                   <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">space_size</span><span class="p">,</span> <span class="n" style="color: #333;">curr_ptr</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1670" 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">

1670

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1670" class="line" lang="c">                   <span class="n" style="color: #333;">curr_ptr</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1671" 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">

1671

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1671" class="line" lang="c"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="1672" 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">

1672

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<td class="diff-line-num new_line old" data-linenumber="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1672" class="line" lang="c">                   <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">curr_ptr</span><span class="p">;</span></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="1673" 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">

1673

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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="LC1673" class="line" lang="c">                   <span class="n" style="color: #333;">curr_ptr</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;">short</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1674" 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">

1674

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1674" class="line" lang="c">                   <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">item_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">curr_ptr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1675" 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">

1675

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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="LC1675" class="line" lang="c">                   <span class="n" style="color: #333;">curr_ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span><span class="p">;</span></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="1676" 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">

1676

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1676" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">curr_ptr</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rdbytes</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1677" 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">

1677

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1677" class="line" lang="c">                           <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: the index cannot be fully loaded : %p > %p + %ld. It may contain format errors or file '%s' may be truncated.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">curr_ptr</span><span class="p">,</span>  <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">rdbytes</span> <span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1678" 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">

1678

</td>

<td class="diff-line-num new_line old" data-linenumber="1505" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1678" class="line" lang="c">                           <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1505

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1505" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">curr_bucks</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1506

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1506" class="line" lang="c">                   <span class="n" style="color: #333;">bucket_bytes</span><span class="p">[</span><span class="n" style="color: #333;">grp_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;">accued_bytes</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1507

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1507" class="line" lang="c">           <span class="n" style="color: #333;">fseeko</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">off_t</span><span class="p">)</span><span class="n" style="color: #333;">fp_curr</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1508

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1508" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1509

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1509" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GEHASH_MEM_PTR_NO</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>

</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="1679" style="width: 35px; color: rgba(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="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1510

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1510" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bucket_bytes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1511

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1511" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">current_bytes</span><span class="o" style="font-weight: 600;"><</span><span class="mh" style="color: #099;">0xff000000u</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1512

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1512" class="line" lang="c">                           <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">current_bytes</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1513

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1513" class="line" lang="c">                           <span class="c1" style="color: #998; font-style: italic;">//SUBREADprintf("Allocating %d buckets : %u\n", i, current_bytes);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1514

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1514" 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;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1515

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1515" class="line" lang="c">                                   <span class="n" style="color: #333;">SUBREADputs</span><span class="p">(</span><span class="n" style="color: #333;">MESSAGE_OUT_OF_MEMORY</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1516

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1516" class="line" lang="c">                                   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1679" style="width: 35px; color: rgba(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="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1517

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1517" class="line" lang="c">                           <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1679

</td>

<td class="diff-line-num new_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1518

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1518" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1680

</td>

<td class="diff-line-num new_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1519

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1519" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1681" 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">

1681

</td>

<td class="diff-line-num new_line old" data-linenumber="1520" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1681" class="line" lang="c">           <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_small_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">curr_ptr</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1682" 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">

1682

</td>

<td class="diff-line-num new_line old" data-linenumber="1520" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1682" class="line" lang="c">           <span class="n" style="color: #333;">curr_ptr</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1683" 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">

1683

</td>

<td class="diff-line-num new_line old" data-linenumber="1520" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1683" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">curr_ptr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rdbytes</span> <span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1684" 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">

1684

</td>

<td class="diff-line-num new_line old" data-linenumber="1520" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1684" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: the index cannot be fully loaded. It may contain format errors or file '%s' may be truncated.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1685" 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">

1685

</td>

<td class="diff-line-num new_line old" data-linenumber="1520" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1685" class="line" lang="c">                   <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1520

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1520" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1521

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1521" class="line" lang="c">           <span class="n" style="color: #333;">grp_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1522

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1522" class="line" lang="c">           <span class="n" style="color: #333;">curr_bucks</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1523

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1523" class="line" lang="c">           <span class="n" style="color: #333;">accued_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1524

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1524" class="line" lang="c">           <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1525

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1525" class="line" lang="c">                   <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">gehash_bucket</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1526

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<pre style="margin: 0;">+<span id="LC1526" class="line" lang="c">                   <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_int32</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1527

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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="c">                   <span class="n" style="color: #333;">load_int32</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//useless for lo: space size</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1528

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<pre style="margin: 0;">+<span id="LC1528" class="line" lang="c">                   <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">space_size</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1529

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<pre style="margin: 0;">+<span id="LC1529" class="line" lang="c">                   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">)</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1530

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1530" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1531

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<pre style="margin: 0;">+<span id="LC1531" class="line" lang="c">                   <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">new_item_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">grp_i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">accued_bytes</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1532

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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="c">                   <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">item_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">grp_i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">accued_bytes</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</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;">short</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1533

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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="c">                   <span class="n" style="color: #333;">read_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">new_item_keys</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">),</span> <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1534

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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="c">                   <span class="n" style="color: #333;">read_length</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">item_values</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">gehash_data_t</span><span class="p">),</span> <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1535

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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1536

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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="c">                           <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: the index is incomplete.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1537

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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="c">                           <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1538

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1538" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1539

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<pre style="margin: 0;">+<span id="LC1539" class="line" lang="c">                   </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1540

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<pre style="margin: 0;">+<span id="LC1540" class="line" lang="c">                   <span class="n" style="color: #333;">accued_bytes</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">current_bytes</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1541

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<pre style="margin: 0;">+<span id="LC1541" class="line" lang="c">                   <span class="n" style="color: #333;">curr_bucks</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1542

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<pre style="margin: 0;">+<span id="LC1542" class="line" lang="c">                   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">curr_bucks</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">per_group_bucks</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(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="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1543

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1543" class="line" lang="c">                           <span class="n" style="color: #333;">curr_bucks</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1544

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1544" class="line" lang="c">                           <span class="n" style="color: #333;">accued_bytes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1545

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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="c">                           <span class="n" style="color: #333;">grp_i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1546

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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1686

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<td class="diff-line-num new_line" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1547

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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1687" 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">

1687

</td>

<td class="diff-line-num new_line old" data-linenumber="1548" 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="LC1687" class="line" lang="c">           <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">curr_ptr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rdbytes</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1688" style="width: 35px; color: rgba(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="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1548

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1548" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1688" style="width: 35px; color: rgba(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="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1549

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<pre style="margin: 0;">+<span id="LC1549" class="line" lang="c">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_small_table</span><span class="p">),</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1688" style="width: 35px; color: rgba(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="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1550

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1550" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rval</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;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: cannot find the table table.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1688" style="width: 35px; color: rgba(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="1551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1551

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<pre style="margin: 0;">+<span id="LC1551" class="line" lang="c">           <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">bucket_bytes</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1688" style="width: 35px; color: rgba(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="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1552

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<pre style="margin: 0;">+<span id="LC1552" class="line" lang="c">           <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1688

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<td class="diff-line-num new_line" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1553

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<pre style="margin: 0;"> <span id="LC1553" class="line" lang="c">           <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1689

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<td class="diff-line-num new_line" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1554

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1554" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1690

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<td class="diff-line-num new_line" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1555

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1555" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1736" style="width: 35px; color: rgba(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="1601" style="width: 35px; color: rgba(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">@@ -1736,7 +1601,10 @@ int gehash_load(gehash_t * the_table, const char fname [])</td>

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<td class="diff-line-num old_line" data-linenumber="1736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1736

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<td class="diff-line-num new_line" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1601

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<pre style="margin: 0;"> <span id="LC1601" class="line" lang="c">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1737

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<td class="diff-line-num new_line" data-linenumber="1602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1602

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1602" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1738

</td>

<td class="diff-line-num new_line" data-linenumber="1603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1603

</td>

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<pre style="margin: 0;"> <span id="LC1603" class="line" lang="c">           <span class="n" style="color: #333;">read_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">is_small_table</span><span class="p">),</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1739" 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">

1739

</td>

<td class="diff-line-num new_line old" data-linenumber="1604" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1739" class="line" lang="c">           <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">read_length</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1740" style="width: 35px; color: rgba(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="1604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1604

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1604" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_length</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1740" style="width: 35px; color: rgba(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="1605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1605

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1605" class="line" lang="c">                   <span class="n" style="color: #333;">SUBREADprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: the index is incomplete.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1740" style="width: 35px; color: rgba(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="1606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1606

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1606" class="line" lang="c">                   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1740" style="width: 35px; color: rgba(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="1607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1607

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1607" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1740

</td>

<td class="diff-line-num new_line" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1608

</td>

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<pre style="margin: 0;"> <span id="LC1608" class="line" lang="c">           <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1741

</td>

<td class="diff-line-num new_line" data-linenumber="1609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1609

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<pre style="margin: 0;"> <span id="LC1609" class="line" lang="c">           <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1742

</td>

<td class="diff-line-num new_line" data-linenumber="1610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1610

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1610" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2027" style="width: 35px; color: rgba(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="1895" style="width: 35px; color: rgba(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">@@ -2027,10 +1895,14 @@ int gehash_dump(gehash_t * the_table, const char fname [])</td>

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<td class="diff-line-num old_line" data-linenumber="2027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2027

</td>

<td class="diff-line-num new_line" data-linenumber="1895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1895

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1895" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2028

</td>

<td class="diff-line-num new_line" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1896

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<pre style="margin: 0;"> <span id="LC1896" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">gehash_destory</span><span class="p">(</span><span class="n" style="color: #333;">gehash_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">the_table</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2029

</td>

<td class="diff-line-num new_line" data-linenumber="1897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1897

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1897" class="line" lang="c"><span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2030" 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">

2030

</td>

<td class="diff-line-num new_line old" data-linenumber="1898" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2030" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2031" style="width: 35px; color: rgba(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="1898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1898

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1898" class="line" lang="c">   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">is_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2031" style="width: 35px; color: rgba(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="1899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1899

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1899" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2031" style="width: 35px; color: rgba(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="1900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1900

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<pre style="margin: 0;">+<span id="LC1900" class="line" lang="c">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">GEHASH_MEM_PTR_NO</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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2031" style="width: 35px; color: rgba(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="1901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1901

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1901" class="line" lang="c">           <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2031" style="width: 35px; color: rgba(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="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1902

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1902" class="line" lang="c">           <span class="n" style="color: #333;">is_ptr</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2031" style="width: 35px; color: rgba(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="1903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1903

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1903" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2031

</td>

<td class="diff-line-num new_line" data-linenumber="1904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1904

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1904" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2032" 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">

2032

</td>

<td class="diff-line-num new_line old" data-linenumber="1905" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2032" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">malloc_ptr</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2033" 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">

2033

</td>

<td class="diff-line-num new_line old" data-linenumber="1905" 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>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2033" class="line" lang="c">   <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</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>

</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="2034" style="width: 35px; color: rgba(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="1905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1905

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1905" 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;">is_ptr</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets_number</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>

</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="2034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2034

</td>

<td class="diff-line-num new_line" data-linenumber="1906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1906

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1906" class="line" lang="c">   <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2035

</td>

<td class="diff-line-num new_line" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1907

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1907" class="line" lang="c">           <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">gehash_bucket</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2036

</td>

<td class="diff-line-num new_line" data-linenumber="1908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1908

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1908" class="line" lang="c">           <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">space_size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2039" style="width: 35px; color: rgba(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="1911" style="width: 35px; color: rgba(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">@@ -2039,6 +1911,7 @@ void gehash_destory(gehash_t * the_table)</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2039

</td>

<td class="diff-line-num new_line" data-linenumber="1911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1911

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1911" class="line" lang="c">                   <span class="n" style="color: #333;">free</span> <span class="p">(</span><span class="n" style="color: #333;">current_bucket</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">item_values</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2040

</td>

<td class="diff-line-num new_line" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1912

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1912" class="line" lang="c">           <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2041

</td>

<td class="diff-line-num new_line" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1913

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1913" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2042" style="width: 35px; color: rgba(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="1914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1914

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1914" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2042

</td>

<td class="diff-line-num new_line" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1915

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1915" class="line" lang="c">   <span class="n" style="color: #333;">free</span> <span class="p">(</span><span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">buckets</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2043

</td>

<td class="diff-line-num new_line" data-linenumber="1916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1916

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1916" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2044

</td>

<td class="diff-line-num new_line" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1917

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1917" class="line" lang="c">   <span class="n" style="color: #333;">the_table</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">current_items</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8668314c149b82a2621dd7e1430711059f36c080">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#8668314c149b82a2621dd7e1430711059f36c080"><strong>src/subread.h</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -270,6 +270,12 @@ struct gehash_bucket {</td>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c">    <span class="n" style="color: #333;">gehash_data_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">item_values</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __MINGW32__</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GEHASH_MEM_PTR_NO (64) </span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GEHASH_MEM_PTR_NO (64*1024) </span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">version_number</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current_items</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">@@ -278,7 +284,7 @@ typedef struct {</td>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">gehash_bucket</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">buckets</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index_gap</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">padding</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC281" 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;">malloc_ptr</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC287" 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;">malloc_ptr</span><span class="idiff left"> </span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">GEHASH_MEM_PTR_NO</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">free_item_only</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">gehash_t</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"></span>

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<br>

</li>

<li id="6eea7570e32aaa0baae17b9c4acbe8539b60b3e5">

<a href="https://salsa.debian.org/med-team/subread/-/compare/ed8de0e16e02b0ff7dc4f36c4c4bebe52d713337...779708682bfd2bfcd7811a9c27a8e500e8f81630#6eea7570e32aaa0baae17b9c4acbe8539b60b3e5"><strong>src/tx-unique.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="85" style="width: 35px; color: rgba(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="85" style="width: 35px; color: rgba(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">@@ -85,7 +85,7 @@ int txunique_load_annotation(txunique_context_t * context){</td>

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<pre style="margin: 0;"> <span id="LC85" 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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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">txunique_process_flat_comp</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;">ex1p</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;">ex2p</span> <span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">txunique_process_flat_comp</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;">ex1p</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;">ex2p</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">me</span></span> <span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c">     <span class="n" style="color: #333;">txunique_exon_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ex1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ex1p</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c">     <span class="n" style="color: #333;">txunique_exon_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ex2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ex2p</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="91" style="width: 35px; color: rgba(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="LC91" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="150" style="width: 35px; color: rgba(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="150" style="width: 35px; color: rgba(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">@@ -150,7 +150,7 @@ void debug_print_edges(ArrayList * exs){</td>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">txunique_process_gene_edge_comp</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;">e1p</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;">e2p</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">txunique_process_gene_edge_comp</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;">e1p</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;">e2p</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ArrayList</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">me</span></span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">_txunique_tmp_edges</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">e1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e1p</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">_txunique_tmp_edges</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">e2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e2p</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">e1</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">base_open_end</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e2</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">base_open_end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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