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GitLab

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<h3>

Steffen Möller pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/biobambam2">Debian Med / biobambam2</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a">fcb2ab68</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-01-24T12:36:54+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.152+dfsg</pre>

</li>

</ul>

<h4>11 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">

.gitignore

</a>

</li>

<li class="file-stats">

<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">

ChangeLog

</a>

</li>

<li class="file-stats">

<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">

configure.ac

</a>

</li>

<li class="file-stats">

<a href="#67e794015a01b8816bd16290e5f8538236da8245">

src/Makefile.am

</a>

</li>

<li class="file-stats">

<a href="#3b06d7c0df977f4386ad9e6694957bfbc058149f">

src/programs/bamauxmerge2.cpp

</a>

</li>

<li class="file-stats">

<a href="#731c8a82cbe64a38ffc549ef39ae18a3c5470e9a">

src/programs/bamconsensus.cpp

</a>

</li>

<li class="file-stats">

<a href="#309ee1cabd82915dbfa35666ebc065bfb115dbac">

src/programs/bamfeaturecount.cpp

</a>

</li>

<li class="file-stats">

<a href="#2bcca0119361ca8be7efd810c71e6bb649b2407e">

src/programs/bamfilterk.cpp

</a>

</li>

<li class="file-stats">

<a href="#12a6e0f37844ed1aef4085c8accc31117da2a7a3">

src/programs/bamtofastq.1

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<li class="file-stats">

<a href="#be752f41aab032268ccb172abc929cf063a40400">

src/programs/bamtofastq.cpp

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<li class="file-stats">

<a href="#b9286f7204613857b6b691786b51e7d8e88e6929">

<span class="new-file">

+

src/programs/vcfreplacecontigs.cpp

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="a5cc2925ca8258af241be7e5b0381edf30266302">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</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="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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,4 +64,5 @@ src/populaterefcache</td>

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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">

64

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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">

64

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">src/vcfconcat</span>

</pre>

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

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

65

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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">

65

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">src/vcfsort</span>

</pre>

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<td class="diff-line-num old_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">

66

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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">

66

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">removespace.sh</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

67

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<td class="diff-line-num new_line old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">src/filtergtf</span></pre>

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

<td class="new_line diff-line-num" style="width: 35px; color: rgba(0,0,0,0.3); 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">\ No newline at end of file</td>

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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">

67

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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="LC67" class="line" lang="plaintext">src/filtergtf</span>

</pre>

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<td class="diff-line-num new old_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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<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">

68

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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="LC68" class="line" lang="plaintext">src/vcfreplacecontigs</span></pre>

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<br>

</li>

<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>

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<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">

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<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">biobambam2 (2.0.152-1) unstable; urgency=medium</span>

</pre>

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2

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

</pre>

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<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">

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<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

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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="LC3" class="line" lang="plaintext">  * update libmaus2 version to 2.0.694</span>

</pre>

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<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">

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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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<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"></span>

</pre>

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<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">

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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"> -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 22 Jan 2020 09:58:27 +0100</span>

</pre>

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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"></span>

</pre>

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<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

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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="LC7" class="line" lang="plaintext">biobambam2 (2.0.151-1) unstable; urgency=medium</span>

</pre>

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8

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

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  * bump libmaus2 version</span>

</pre>

</td>

</tr>

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<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">

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10

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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="LC10" 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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 21 Jan 2020 16:41:38 +0100</span>

</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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

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

<pre style="margin: 0;">+<span id="LC12" 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="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">biobambam2 (2.0.150-1) 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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

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

<pre style="margin: 0;">+<span id="LC14" 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="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

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

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">  * Add cols (line wrapping) option in bamtofastq</span>

</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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

</td>

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

<pre style="margin: 0;">+<span id="LC16" 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="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">

17

</td>

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 07 Jan 2020 16:37:02 +0100</span>

</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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

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

<pre style="margin: 0;">+<span id="LC18" 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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

</td>

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

<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">biobambam2 (2.0.149-1) 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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

</td>

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

<pre style="margin: 0;">+<span id="LC20" 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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

</td>

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">  * use kmerCallbackPosFR instead of kmerCallbackPos in bamfilterk</span>

</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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

</td>

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

<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">  * Add vcfreplacecontigs program</span>

</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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

</td>

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

<pre style="margin: 0;">+<span id="LC23" 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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

</td>

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 07 Jan 2020 09:02:29 +0100</span>

</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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

</td>

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

<pre style="margin: 0;">+<span id="LC25" 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="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

</td>

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">biobambam2 (2.0.148-1) 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="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

</td>

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

<pre style="margin: 0;">+<span id="LC27" 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="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

</td>

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

<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">  * compute maximum depth in bamfeaturecount</span>

</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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

</td>

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

<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">  * fix output of wrong reference id in bamfeaturecount if GTF chrom set is a subset of BAM chrom set</span>

</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="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

</td>

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

<pre style="margin: 0;">+<span id="LC30" 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="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">

31

</td>

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

<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 13 Nov 2019 12:53:00 +0100</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>

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1

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33

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">biobambam2 (2.0.147-1) unstable; urgency=medium</span>

</pre>

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2

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34

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>

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3

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">  * fix heap comparisons in bamconsensus</span>

</pre>

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<br>

</li>

<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">AC_INIT(biobambam2,2.0.1<span class="idiff left right">47</span>,[germant@miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])</span>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT(biobambam2,2.0.1<span class="idiff left right">52</span>,[germant@miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])</span>

</pre>

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2

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2

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

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3

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3

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

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4

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4

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -165,7 +165,7 @@ if test ! -z "${with_libmaus2}" ; then</td>

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165

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

</pre>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext">fi</span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); 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="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext">PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.6<span class="idiff left right">83</span>])</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="169" style="width: 35px; color: rgba(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="168" style="width: 35px; color: rgba(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="LC168" class="line" lang="plaintext">PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.6<span class="idiff left right">94</span>])</span>

</pre>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

170

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<td class="diff-line-num new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC170" class="line" lang="plaintext">if test ! -z "${with_libmaus2}" ; then</span>

</pre>

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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="plaintext">    if test ! -z "${PKGCONFIGPATHSAVE}" ; then</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); 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="300" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -300,7 +300,7 @@ if test "${have_libmaus2_irods}" = "yes" ; then</td>

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<td class="diff-line-num old_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC300" class="line" lang="plaintext">            fi</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC301" class="line" lang="plaintext">    fi</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC302" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="plaintext">    PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.6<span class="idiff left right">83</span>])</span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">    PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.6<span class="idiff left right">94</span>])</span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="plaintext">    LIBMAUS2IRODSCPPFLAGS="${libmaus2irods_CFLAGS}"</span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="plaintext">    LIBMAUS2IRODSLIBS="${libmaus2irods_LIBS}"</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="463" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -463,7 +463,7 @@ AC_ARG_ENABLE(install_uncommon,</td>

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<td class="diff-line-num old_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC463" class="line" lang="plaintext">        AS_HELP_STRING([--enable-install-uncommon],[enable installation of some uncommon programs (default no)]),</span>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="plaintext">        [install_uncommon=${enableval}],[install_uncommon=no])</span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC466" class="line" lang="plaintext">UNCOMMON="bamfilter bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext">UNCOMMON="bamfilter bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus<span class="idiff left right"> vcfreplacecontigs</span>"</span>

</pre>

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467

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<pre style="margin: 0;"> <span id="LC467" class="line" lang="plaintext">UNCOMMONINSTALLED=</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC468" class="line" lang="plaintext">UNCOMMONUNINSTALLED=</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

469

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<td class="diff-line-num new_line" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="plaintext">if test "${install_uncommon}" = "yes" ; then</span>

</pre>

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<br>

</li>

<li id="67e794015a01b8816bd16290e5f8538236da8245">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#67e794015a01b8816bd16290e5f8538236da8245"><strong>src/Makefile.am</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -138,6 +138,7 @@ EXTRA_PROGRAMS = blastnxmltobam \</td>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="make"> vcfpatchcontigprepend <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); 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="139" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC139" class="line" lang="make"> vcfconcat <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="make"> vcfsort <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="141" style="width: 35px; color: rgba(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="141" style="width: 35px; color: rgba(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="LC141" class="line" lang="make"> vcfreplacecontigs <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); 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="142" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC142" class="line" lang="make"> filtergtf</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC143" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

143

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="make"><span class="nv" style="color: #008080;">populaterefcache_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> programs/populaterefcache.cpp biobambam2/Licensing.cpp</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); 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="601" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -600,6 +601,11 @@ vcfsort_LDADD = ${LIBMAUS2LIBS}</td>

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<td class="diff-line-num old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); 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="601" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC601" class="line" lang="make"><span class="nv" style="color: #008080;">vcfsort_LDFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${AM_CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2LDFLAGS}</span> <span class="nv" style="color: #008080;">${AM_LDFLAGS}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); 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="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

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<pre style="margin: 0;"> <span id="LC602" class="line" lang="make"><span class="nv" style="color: #008080;">vcfsort_CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${AM_CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2CPPFLAGS}</span></span>

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<td class="diff-line-num old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

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<td class="diff-line-num new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC603" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="603" style="width: 35px; color: rgba(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="604" style="width: 35px; color: rgba(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="LC604" class="line" lang="make"><span class="nv" style="color: #008080;">vcfreplacecontigs_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> programs/vcfreplacecontigs.cpp biobambam2/Licensing.cpp</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="603" style="width: 35px; color: rgba(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="605" style="width: 35px; color: rgba(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="LC605" class="line" lang="make"><span class="nv" style="color: #008080;">vcfreplacecontigs_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${LIBMAUS2LIBS}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="603" style="width: 35px; color: rgba(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="606" style="width: 35px; color: rgba(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="LC606" class="line" lang="make"><span class="nv" style="color: #008080;">vcfreplacecontigs_LDFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${AM_CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2LDFLAGS}</span> <span class="nv" style="color: #008080;">${AM_LDFLAGS}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="603" style="width: 35px; color: rgba(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="607" style="width: 35px; color: rgba(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="LC607" class="line" lang="make"><span class="nv" style="color: #008080;">vcfreplacecontigs_CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${AM_CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2CPPFLAGS}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="603" style="width: 35px; color: rgba(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="608" style="width: 35px; color: rgba(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="LC608" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC609" class="line" lang="make"><span class="nv" style="color: #008080;">bamfiltereofblocks_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> programs/bamfiltereofblocks.cpp biobambam2/Licensing.cpp biobambam2/RunEOFFilter.cpp</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC610" class="line" lang="make"><span class="nv" style="color: #008080;">bamfiltereofblocks_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${LIBMAUS2LIBS}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

605

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<td class="diff-line-num new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC611" class="line" lang="make"><span class="nv" style="color: #008080;">bamfiltereofblocks_LDFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${AM_CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2LDFLAGS}</span> <span class="nv" style="color: #008080;">${AM_LDFLAGS}</span></span>

</pre>

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<br>

</li>

<li id="3b06d7c0df977f4386ad9e6694957bfbc058149f">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#3b06d7c0df977f4386ad9e6694957bfbc058149f"><strong>src/programs/bamauxmerge2.cpp</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,6 +47,7 @@</td>

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<td class="diff-line-num old_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">

47

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/LELoad.hpp></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); 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="48" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC48" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/fastx/FastAReader.hpp></span></span>

</pre>

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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="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">

50

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/StrCmpNum.hpp></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <biobambam2/BamBamConfig.hpp></span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <biobambam2/Licensing.hpp></span></span>

</pre>

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<br>

</li>

<li id="731c8a82cbe64a38ffc549ef39ae18a3c5470e9a">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#731c8a82cbe64a38ffc549ef39ae18a3c5470e9a"><strong>src/programs/bamconsensus.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1854" style="width: 35px; color: rgba(0,0,0,0.3); 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="1854" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1854,7 +1854,6 @@ std::vector<ConsensusPart> handleConsensus(</td>

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<pre style="margin: 0;"> <span id="LC1854" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">              }</span></span>

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<td class="diff-line-num old_line" data-linenumber="1855" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1855" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">              #endif</span></span>

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<td class="diff-line-num old_line" data-linenumber="1856" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1856" class="line" lang="cpp"></span>

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<td class="diff-line-num old old_line" data-linenumber="1857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1857" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1858" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1857" class="line" lang="cpp">         <span class="c1" style="color: #998; font-style: italic;">// get set of branch points</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1859" style="width: 35px; color: rgba(0,0,0,0.3); 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="1858" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1858" class="line" lang="cpp">         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BranchPoint</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">SBP</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1860" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1859" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</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;">VBL</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1873" style="width: 35px; color: rgba(0,0,0,0.3); 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="1872" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1873,17 +1872,22 @@ std::vector<ConsensusPart> handleConsensus(</td>

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<td class="diff-line-num old_line" data-linenumber="1873" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1872" class="line" lang="cpp">                 <span class="n" style="color: #333;">BranchPoint</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">from</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1874" style="width: 35px; color: rgba(0,0,0,0.3); 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="1873" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1873" class="line" lang="cpp">                 <span class="n" style="color: #333;">BranchPoint</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">to</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1875" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1874" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1876" style="width: 35px; color: rgba(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="LC1875" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// get from id in branch point vector</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1876" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1876" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">fromid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lower_bound</span><span class="p">(</span><span class="n" style="color: #333;">VBP</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">VBP</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">VBP</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span><span class="n" style="color: #333;">from</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">VBP</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC1877" class="line" lang="cpp">                 <span class="n" style="color: #333;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">fromid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">VBP</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">VBP</span><span class="p">[</span><span class="n" style="color: #333;">fromid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">from</span> <span class="p">);</span></span>

</pre>

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1878

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<pre style="margin: 0;">+<span id="LC1878" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// get to id in branch point vector</span></span>

</pre>

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1878

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<td class="diff-line-num new_line" data-linenumber="1879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1879

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<pre style="margin: 0;"> <span id="LC1879" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">toid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lower_bound</span><span class="p">(</span><span class="n" style="color: #333;">VBP</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">VBP</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">VBP</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span><span class="n" style="color: #333;">to</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">VBP</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1879" style="width: 35px; color: rgba(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="1880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1880

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<pre style="margin: 0;">+<span id="LC1880" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">//</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1879

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<td class="diff-line-num new_line" data-linenumber="1881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1881

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<pre style="margin: 0;"> <span id="LC1881" class="line" lang="cpp">                 <span class="n" style="color: #333;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">toid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">VBP</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">VBP</span><span class="p">[</span><span class="n" style="color: #333;">toid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">to</span> <span class="p">);</span></span>

</pre>

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1880

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<td class="diff-line-num new_line" data-linenumber="1882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1882

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<pre style="margin: 0;"> <span id="LC1882" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1883

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<pre style="margin: 0;">+<span id="LC1883" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// store link (1 based)</span></span>

</pre>

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1881

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<td class="diff-line-num new_line" data-linenumber="1884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1884

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<pre style="margin: 0;"> <span id="LC1884" class="line" lang="cpp">                 <span class="n" style="color: #333;">edgeMap</span><span class="p">[</span><span class="n" style="color: #333;">fromid</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;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">toid</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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1882

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<td class="diff-line-num new_line" data-linenumber="1885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1885

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<pre style="margin: 0;"> <span id="LC1885" class="line" lang="cpp">         <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1883

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<td class="diff-line-num new_line" data-linenumber="1886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1886

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<pre style="margin: 0;"> <span id="LC1886" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1884

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<td class="diff-line-num new_line" data-linenumber="1887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1887

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<pre style="margin: 0;"> <span id="LC1887" class="line" lang="cpp">         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Vcomp</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1885

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<td class="diff-line-num new_line" data-linenumber="1888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1888

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<pre style="margin: 0;"> <span id="LC1888" class="line" lang="cpp">         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Vcompmap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1886

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<td class="diff-line-num new_line" data-linenumber="1889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1889

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<pre style="margin: 0;"> <span id="LC1889" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1887" style="width: 35px; color: rgba(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="1890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1890

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<pre style="margin: 0;">+<span id="LC1890" class="line" lang="cpp">         <span class="c1" style="color: #998; font-style: italic;">// compute connected components</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1887

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<td class="diff-line-num new_line" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1891

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<pre style="margin: 0;"> <span id="LC1891" class="line" lang="cpp">         <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1888

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<td class="diff-line-num new_line" data-linenumber="1892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1892

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<pre style="margin: 0;"> <span id="LC1892" class="line" lang="cpp">                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">unseen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1889

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<td class="diff-line-num new_line" data-linenumber="1893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1893

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<pre style="margin: 0;"> <span id="LC1893" class="line" lang="cpp">                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">redgeMap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1900" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1900,7 +1904,6 @@ std::vector<ConsensusPart> handleConsensus(</td>

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<td class="diff-line-num old_line" data-linenumber="1900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1900

</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="cpp">                         <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1901

</td>

<td class="diff-line-num new_line" data-linenumber="1905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1905

</td>

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

<pre style="margin: 0;"> <span id="LC1905" class="line" lang="cpp">                 <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1902

</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="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1903

</td>

<td class="diff-line-num new_line old" data-linenumber="1907" style="width: 35px; color: rgba(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="LC1903" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_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="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

</td>

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

<pre style="margin: 0;"> <span id="LC1907" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">unseen</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1905

</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="cpp">                 <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_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="diff-line-num new_line" data-linenumber="1909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1909

</td>

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

<pre style="margin: 0;"> <span id="LC1909" class="line" lang="cpp">                         <span class="c" style="color: #998; font-style: italic;">#if 0</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1945" style="width: 35px; color: rgba(0,0,0,0.3); 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="1948" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1945,9 +1948,11 @@ std::vector<ConsensusPart> handleConsensus(</td>

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<td class="diff-line-num old_line" data-linenumber="1945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1945

</td>

<td class="diff-line-num new_line" data-linenumber="1948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1948

</td>

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

<pre style="margin: 0;"> <span id="LC1948" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1946

</td>

<td class="diff-line-num new_line" data-linenumber="1949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1949

</td>

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

<pre style="margin: 0;"> <span id="LC1949" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">V</span><span class="p">(</span><span class="n" style="color: #333;">component</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">component</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1947

</td>

<td class="diff-line-num new_line" data-linenumber="1950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1950

</td>

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

<pre style="margin: 0;"> <span id="LC1950" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1951

</td>

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

<pre style="margin: 0;">+<span id="LC1951" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">// set branch point id to component map</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1948

</td>

<td class="diff-line-num new_line" data-linenumber="1952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1952

</td>

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

<pre style="margin: 0;"> <span id="LC1952" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</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;">V</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</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="1949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1949

</td>

<td class="diff-line-num new_line" data-linenumber="1953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1953

</td>

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

<pre style="margin: 0;"> <span id="LC1953" class="line" lang="cpp">                                 <span class="n" style="color: #333;">Vcompmap</span><span class="p">[</span><span class="n" style="color: #333;">V</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;">Vcomp</span><span class="p">.</span><span class="n" style="color: #333;">size</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="1950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1950

</td>

<td class="diff-line-num new_line" data-linenumber="1954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1954

</td>

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

<pre style="margin: 0;"> <span id="LC1954" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1955

</td>

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

<pre style="margin: 0;">+<span id="LC1955" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">// push connected component</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1951

</td>

<td class="diff-line-num new_line" data-linenumber="1956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1956

</td>

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

<pre style="margin: 0;"> <span id="LC1956" class="line" lang="cpp">                         <span class="n" style="color: #333;">Vcomp</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">V</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="1952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1952

</td>

<td class="diff-line-num new_line" data-linenumber="1957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1957

</td>

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

<pre style="margin: 0;"> <span id="LC1957" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1953

</td>

<td class="diff-line-num new_line" data-linenumber="1958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1958

</td>

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

<pre style="margin: 0;"> <span id="LC1958" class="line" lang="cpp">                         <span class="c" style="color: #998; font-style: italic;">#if 0</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1959" style="width: 35px; color: rgba(0,0,0,0.3); 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="1964" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1959,6 +1964,7 @@ std::vector<ConsensusPart> handleConsensus(</td>

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<td class="diff-line-num old_line" data-linenumber="1959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1959

</td>

<td class="diff-line-num new_line" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1964

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<pre style="margin: 0;"> <span id="LC1964" class="line" lang="cpp">                 <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1960

</td>

<td class="diff-line-num new_line" data-linenumber="1965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1965

</td>

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<pre style="margin: 0;"> <span id="LC1965" class="line" lang="cpp">         <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1961

</td>

<td class="diff-line-num new_line" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1966

</td>

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

<pre style="margin: 0;"> <span id="LC1966" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1967

</td>

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

<pre style="margin: 0;">+<span id="LC1967" class="line" lang="cpp">         <span class="c1" style="color: #998; font-style: italic;">// consider connected components</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1962

</td>

<td class="diff-line-num new_line" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1968

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

<pre style="margin: 0;"> <span id="LC1968" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">z</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;">z</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Vcomp</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">z</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1963

</td>

<td class="diff-line-num new_line" data-linenumber="1969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1969

</td>

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

<pre style="margin: 0;"> <span id="LC1969" class="line" lang="cpp">         <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1964

</td>

<td class="diff-line-num new_line" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1970

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

<pre style="margin: 0;"> <span id="LC1970" class="line" lang="cpp">                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</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;">Vcomp</span><span class="p">[</span><span class="n" style="color: #333;">z</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); 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="1974" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1968,13 +1974,16 @@ std::vector<ConsensusPart> handleConsensus(</td>

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<td class="diff-line-num old_line" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1968

</td>

<td class="diff-line-num new_line" data-linenumber="1974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1974

</td>

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

<pre style="margin: 0;"> <span id="LC1974" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">maxx</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>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1969

</td>

<td class="diff-line-num new_line" data-linenumber="1975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1975

</td>

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

<pre style="margin: 0;"> <span id="LC1975" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">maxu</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>

</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="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1970

</td>

<td class="diff-line-num new_line" data-linenumber="1976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1976

</td>

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

<pre style="margin: 0;"> <span id="LC1976" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1977

</td>

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

<pre style="margin: 0;">+<span id="LC1977" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// iterate over branch points in component</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1971

</td>

<td class="diff-line-num new_line" data-linenumber="1978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1978

</td>

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

<pre style="margin: 0;"> <span id="LC1978" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">y</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;">y</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;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">y</span> <span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1972

</td>

<td class="diff-line-num new_line" data-linenumber="1979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1979

</td>

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

<pre style="margin: 0;"> <span id="LC1979" class="line" lang="cpp">                 <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="1973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1973

</td>

<td class="diff-line-num new_line" data-linenumber="1980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1980

</td>

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

<pre style="margin: 0;"> <span id="LC1980" class="line" lang="cpp">                         <span class="n" style="color: #333;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">V</span><span class="p">[</span><span class="n" style="color: #333;">y</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>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1981

</td>

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

<pre style="margin: 0;">+<span id="LC1981" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">// get branch point</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1974

</td>

<td class="diff-line-num new_line" data-linenumber="1982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1982

</td>

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

<pre style="margin: 0;"> <span id="LC1982" class="line" lang="cpp">                         <span class="n" style="color: #333;">BranchPoint</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VBP</span><span class="p">[</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="n" style="color: #333;">y</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" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1975

</td>

<td class="diff-line-num new_line" data-linenumber="1983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1983

</td>

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

<pre style="margin: 0;"> <span id="LC1983" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1976

</td>

<td class="diff-line-num new_line" data-linenumber="1984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1984

</td>

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

<pre style="margin: 0;"> <span id="LC1984" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BranchLink</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">it</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="1977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1977

</td>

<td class="diff-line-num new_line" data-linenumber="1985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1985

</td>

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

<pre style="margin: 0;"> <span id="LC1985" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1986

</td>

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

<pre style="margin: 0;">+<span id="LC1986" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">// get branch links originating from BP</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1978

</td>

<td class="diff-line-num new_line" data-linenumber="1987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1987

</td>

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

<pre style="margin: 0;"> <span id="LC1987" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">it</span><span class="p">,</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">equal_range</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="1979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1979

</td>

<td class="diff-line-num new_line" data-linenumber="1988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1988

</td>

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

<pre style="margin: 0;"> <span id="LC1988" class="line" lang="cpp">                                 <span class="n" style="color: #333;">VBL</span><span class="p">.</span><span class="n" style="color: #333;">begin</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="1980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1980

</td>

<td class="diff-line-num new_line" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1989

</td>

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

<pre style="margin: 0;"> <span id="LC1989" class="line" lang="cpp">                                 <span class="n" style="color: #333;">VBL</span><span class="p">.</span><span class="n" style="color: #333;">end</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="1982" style="width: 35px; color: rgba(0,0,0,0.3); 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="1991" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1982,9 +1991,12 @@ std::vector<ConsensusPart> handleConsensus(</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1982

</td>

<td class="diff-line-num new_line" data-linenumber="1991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1991

</td>

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

<pre style="margin: 0;"> <span id="LC1991" class="line" lang="cpp">                                 <span class="n" style="color: #333;">BranchLinkFromComparator</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="1983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1983

</td>

<td class="diff-line-num new_line" data-linenumber="1992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1992

</td>

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

<pre style="margin: 0;"> <span id="LC1992" class="line" lang="cpp">                         <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="1984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1984

</td>

<td class="diff-line-num new_line" data-linenumber="1993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1993

</td>

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

<pre style="margin: 0;"> <span id="LC1993" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1994

</td>

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

<pre style="margin: 0;">+<span id="LC1994" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">// iterate over branch links</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1985

</td>

<td class="diff-line-num new_line" data-linenumber="1995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1995

</td>

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

<pre style="margin: 0;"> <span id="LC1995" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">x</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="1986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1986

</td>

<td class="diff-line-num new_line" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1996

</td>

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

<pre style="margin: 0;"> <span id="LC1996" class="line" lang="cpp">                         <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="1987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1997

</td>

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

<pre style="margin: 0;">+<span id="LC1997" class="line" lang="cpp">                                 <span class="c1" style="color: #998; font-style: italic;">// get link</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1987

</td>

<td class="diff-line-num new_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1998

</td>

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

<pre style="margin: 0;"> <span id="LC1998" class="line" lang="cpp">                                 <span class="n" style="color: #333;">BranchLink</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BL</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</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="1988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1999

</td>

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

<pre style="margin: 0;">+<span id="LC1999" class="line" lang="cpp">                                 <span class="c1" style="color: #998; font-style: italic;">// get kmer links</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1988

</td>

<td class="diff-line-num new_line" data-linenumber="2000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2000

</td>

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

<pre style="margin: 0;"> <span id="LC2000" class="line" lang="cpp">                                 <span class="n" style="color: #333;">KmerLink</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">KL_A</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AKLBL</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">BL</span><span class="p">.</span><span class="n" style="color: #333;">link_start</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="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1989

</td>

<td class="diff-line-num new_line" data-linenumber="2001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2001

</td>

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

<pre style="margin: 0;"> <span id="LC2001" class="line" lang="cpp">                                 <span class="n" style="color: #333;">KmerLink</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">KL_E</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AKLBL</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">BL</span><span class="p">.</span><span class="n" style="color: #333;">link_end</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="1990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1990

</td>

<td class="diff-line-num new_line" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2002

</td>

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

<pre style="margin: 0;"> <span id="LC2002" class="line" lang="cpp"></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="1993" style="width: 35px; color: rgba(0,0,0,0.3); 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="2005" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1993,8 +2005,10 @@ std::vector<ConsensusPart> handleConsensus(</td>

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

<td class="diff-line-num old_line" data-linenumber="1993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1993

</td>

<td class="diff-line-num new_line" data-linenumber="2005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2005

</td>

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

<pre style="margin: 0;"> <span id="LC2005" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1994

</td>

<td class="diff-line-num new_line" data-linenumber="2006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2006

</td>

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

<pre style="margin: 0;"> <span id="LC2006" class="line" lang="cpp">                                 <span class="c1" style="color: #998; font-style: italic;">// std::cerr << BL << std::endl;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1995

</td>

<td class="diff-line-num new_line" data-linenumber="2007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2007

</td>

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

<pre style="margin: 0;"> <span id="LC2007" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2008

</td>

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

<pre style="margin: 0;">+<span id="LC2008" class="line" lang="cpp">                                 <span class="c1" style="color: #998; font-style: italic;">// iterate over kmer links on branch link</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1996

</td>

<td class="diff-line-num new_line" data-linenumber="2009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2009

</td>

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

<pre style="margin: 0;"> <span id="LC2009" class="line" lang="cpp">                                 <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="n" style="color: #333;">KmerLink</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">KL_C</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">KL_A</span><span class="p">;</span> <span class="n" style="color: #333;">KL_C</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">KL_E</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">KL_C</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="1997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1997

</td>

<td class="diff-line-num new_line" data-linenumber="2010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2010

</td>

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

<pre style="margin: 0;"> <span id="LC2010" class="line" lang="cpp">                                 <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="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2011

</td>

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

<pre style="margin: 0;">+<span id="LC2011" class="line" lang="cpp">                                         <span class="c1" style="color: #998; font-style: italic;">// get frequency of from and to</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1998

</td>

<td class="diff-line-num new_line" data-linenumber="2012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2012

</td>

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

<pre style="margin: 0;"> <span id="LC2012" class="line" lang="cpp">                                         <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">fromfreq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">KL_C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fromfreq</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="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1999

</td>

<td class="diff-line-num new_line" data-linenumber="2013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2013

</td>

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

<pre style="margin: 0;"> <span id="LC2013" class="line" lang="cpp">                                         <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">tofreq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">KL_C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tofreq</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="2000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2000

</td>

<td class="diff-line-num new_line" data-linenumber="2014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2014

</td>

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

<pre style="margin: 0;"> <span id="LC2014" class="line" lang="cpp"></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="2021" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2021,10 +2035,12 @@ std::vector<ConsensusPart> handleConsensus(</td>

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

<td class="diff-line-num old_line" data-linenumber="2021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2021

</td>

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

<pre style="margin: 0;"> <span id="LC2035" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2022

</td>

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

<pre style="margin: 0;"> <span id="LC2036" class="line" lang="cpp">                 <span class="n" style="color: #333;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">maxfreq</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="2023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2023

</td>

<td class="diff-line-num new_line" data-linenumber="2037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2037

</td>

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

<pre style="margin: 0;"> <span id="LC2037" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2038

</td>

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

<pre style="margin: 0;">+<span id="LC2038" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// get branch point carying maximum frequency link</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2024

</td>

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

<pre style="margin: 0;"> <span id="LC2039" class="line" lang="cpp">                 <span class="n" style="color: #333;">BranchPoint</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VBP</span><span class="p">[</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="n" style="color: #333;">maxy</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" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2025

</td>

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

<pre style="margin: 0;"> <span id="LC2040" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2026

</td>

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

<pre style="margin: 0;"> <span id="LC2041" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BranchLink</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">it</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="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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2042" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2043

</td>

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

<pre style="margin: 0;">+<span id="LC2043" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// get vector of links originating from BP</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="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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2044" class="line" lang="cpp">                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">it</span><span class="p">,</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">equal_range</span><span class="p">(</span></span>

</pre>

</td>

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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="2045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2045

</td>

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

<pre style="margin: 0;"> <span id="LC2045" class="line" lang="cpp">                         <span class="n" style="color: #333;">VBL</span><span class="p">.</span><span class="n" style="color: #333;">begin</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="2030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2030

</td>

<td class="diff-line-num new_line" data-linenumber="2046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2046

</td>

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

<pre style="margin: 0;"> <span id="LC2046" class="line" lang="cpp">                         <span class="n" style="color: #333;">VBL</span><span class="p">.</span><span class="n" style="color: #333;">end</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="2048" style="width: 35px; color: rgba(0,0,0,0.3); 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="2064" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2048,8 +2064,10 @@ std::vector<ConsensusPart> handleConsensus(</td>

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

<td class="diff-line-num old_line" data-linenumber="2048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2048

</td>

<td class="diff-line-num new_line" data-linenumber="2064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2064

</td>

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

<pre style="margin: 0;"> <span id="LC2064" class="line" lang="cpp">                 <span class="n" style="color: #333;">BranchLink</span> <span class="n" style="color: #333;">curBL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">[</span><span class="n" style="color: #333;">maxx</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="2049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2049

</td>

<td class="diff-line-num new_line" data-linenumber="2065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2065

</td>

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

<pre style="margin: 0;"> <span id="LC2065" class="line" lang="cpp">                 <span class="n" style="color: #333;">VBLmax</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">curBL</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="2050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2050

</td>

<td class="diff-line-num new_line" data-linenumber="2066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2066

</td>

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

<pre style="margin: 0;"> <span id="LC2066" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2067

</td>

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

<pre style="margin: 0;">+<span id="LC2067" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// follow backward links from curBL</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="2051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2051

</td>

<td class="diff-line-num new_line" data-linenumber="2068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2068

</td>

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

<pre style="margin: 0;"> <span id="LC2068" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">true</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="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

</td>

<td class="diff-line-num new_line" data-linenumber="2069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2069

</td>

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

<pre style="margin: 0;"> <span id="LC2069" class="line" lang="cpp">                 <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="2053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2070

</td>

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

<pre style="margin: 0;">+<span id="LC2070" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">// look for links</span></span>

</pre>

</td>

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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

</td>

<td class="diff-line-num new_line" data-linenumber="2071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2071

</td>

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

<pre style="margin: 0;"> <span id="LC2071" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">it</span><span class="p">,</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LP</span> <span class="o" style="font-weight: 600;">=</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="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

</td>

<td class="diff-line-num new_line" data-linenumber="2072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2072

</td>

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

<pre style="margin: 0;"> <span id="LC2072" class="line" lang="cpp">                                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">equal_range</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="2055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2055

</td>

<td class="diff-line-num new_line" data-linenumber="2073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2073

</td>

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

<pre style="margin: 0;"> <span id="LC2073" class="line" lang="cpp">                                         <span class="n" style="color: #333;">VBLto</span><span class="p">.</span><span class="n" style="color: #333;">begin</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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2076" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2058,8 +2076,10 @@ std::vector<ConsensusPart> handleConsensus(</td>

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

<td class="diff-line-num old_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">

2058

</td>

<td class="diff-line-num new_line" data-linenumber="2076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2076

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<pre style="margin: 0;"> <span id="LC2076" class="line" lang="cpp">                                         <span class="n" style="color: #333;">BranchLinkToComparator</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2059

</td>

<td class="diff-line-num new_line" data-linenumber="2077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2077

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<pre style="margin: 0;"> <span id="LC2077" class="line" lang="cpp">                                 <span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2060

</td>

<td class="diff-line-num new_line" data-linenumber="2078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2078

</td>

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

<pre style="margin: 0;"> <span id="LC2078" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2079

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<pre style="margin: 0;">+<span id="LC2079" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">// if any</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2061

</td>

<td class="diff-line-num new_line" data-linenumber="2080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2080

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<pre style="margin: 0;"> <span id="LC2080" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">LP</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">LP</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2062

</td>

<td class="diff-line-num new_line" data-linenumber="2081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2081

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

<pre style="margin: 0;"> <span id="LC2081" class="line" lang="cpp">                         <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2082

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<pre style="margin: 0;">+<span id="LC2082" class="line" lang="cpp">                                 <span class="c1" style="color: #998; font-style: italic;">// look for maximum weight</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2063

</td>

<td class="diff-line-num new_line" data-linenumber="2083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2083

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<pre style="margin: 0;"> <span id="LC2083" class="line" lang="cpp">                                 <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2064

</td>

<td class="diff-line-num new_line" data-linenumber="2084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2084

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<pre style="margin: 0;"> <span id="LC2084" class="line" lang="cpp">                                 <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">maxi</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>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2065

</td>

<td class="diff-line-num new_line" data-linenumber="2085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2085

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

<pre style="margin: 0;"> <span id="LC2085" class="line" lang="cpp">                                 <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</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;">LP</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">LP</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2079" style="width: 35px; color: rgba(0,0,0,0.3); 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="2099" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2079,6 +2099,7 @@ std::vector<ConsensusPart> handleConsensus(</td>

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<td class="diff-line-num old_line" data-linenumber="2079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2079

</td>

<td class="diff-line-num new_line" data-linenumber="2099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2099

</td>

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

<pre style="margin: 0;"> <span id="LC2099" class="line" lang="cpp">                         <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="2080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2080

</td>

<td class="diff-line-num new_line" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2100

</td>

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

<pre style="margin: 0;"> <span id="LC2100" class="line" lang="cpp">                 <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="2081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2081

</td>

<td class="diff-line-num new_line" data-linenumber="2101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2101

</td>

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

<pre style="margin: 0;"> <span id="LC2101" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2102

</td>

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

<pre style="margin: 0;">+<span id="LC2102" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// reverse path (we were going backward)</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="2082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2082

</td>

<td class="diff-line-num new_line" data-linenumber="2103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2103

</td>

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

<pre style="margin: 0;"> <span id="LC2103" class="line" lang="cpp">                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reverse</span><span class="p">(</span><span class="n" style="color: #333;">VBLmax</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">VBLmax</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2083

</td>

<td class="diff-line-num new_line" data-linenumber="2104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2104

</td>

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

<pre style="margin: 0;"> <span id="LC2104" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2084

</td>

<td class="diff-line-num new_line" data-linenumber="2105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2105

</td>

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

<pre style="margin: 0;"> <span id="LC2105" class="line" lang="cpp">                 <span class="n" style="color: #333;">curBL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">[</span><span class="n" style="color: #333;">maxx</span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2086" style="width: 35px; color: rgba(0,0,0,0.3); 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="2107" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2086,8 +2107,10 @@ std::vector<ConsensusPart> handleConsensus(</td>

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<td class="diff-line-num old_line" data-linenumber="2086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2086

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<td class="diff-line-num new_line" data-linenumber="2107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2107

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<pre style="margin: 0;"> <span id="LC2107" class="line" lang="cpp">                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BranchLink</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">VBLfrom</span><span class="p">(</span><span class="n" style="color: #333;">VBL</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2087

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<td class="diff-line-num new_line" data-linenumber="2108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2108

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<pre style="margin: 0;"> <span id="LC2108" class="line" lang="cpp">                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">VBLfrom</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">VBLfrom</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span><span class="n" style="color: #333;">BranchLinkFromComparator</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2088

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<td class="diff-line-num new_line" data-linenumber="2109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2109

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<pre style="margin: 0;"> <span id="LC2109" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2110

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<pre style="margin: 0;">+<span id="LC2110" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// follow forward</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2089

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<td class="diff-line-num new_line" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2111

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<pre style="margin: 0;"> <span id="LC2111" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">true</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2090

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<td class="diff-line-num new_line" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2112

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<pre style="margin: 0;"> <span id="LC2112" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2113

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<pre style="margin: 0;">+<span id="LC2113" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">// look for extensions</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2091

</td>

<td class="diff-line-num new_line" data-linenumber="2114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2114

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<pre style="margin: 0;"> <span id="LC2114" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">it</span><span class="p">,</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LP</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2092

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<td class="diff-line-num new_line" data-linenumber="2115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2115

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<pre style="margin: 0;"> <span id="LC2115" class="line" lang="cpp">                                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">equal_range</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2093

</td>

<td class="diff-line-num new_line" data-linenumber="2116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2116

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<pre style="margin: 0;"> <span id="LC2116" class="line" lang="cpp">                                         <span class="n" style="color: #333;">VBLfrom</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2096" style="width: 35px; color: rgba(0,0,0,0.3); 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="2119" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2096,8 +2119,10 @@ std::vector<ConsensusPart> handleConsensus(</td>

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<td class="diff-line-num old_line" data-linenumber="2096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2096

</td>

<td class="diff-line-num new_line" data-linenumber="2119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2119

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<pre style="margin: 0;"> <span id="LC2119" class="line" lang="cpp">                                         <span class="n" style="color: #333;">BranchLinkFromComparator</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2097

</td>

<td class="diff-line-num new_line" data-linenumber="2120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2120

</td>

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

<pre style="margin: 0;"> <span id="LC2120" class="line" lang="cpp">                                 <span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2098

</td>

<td class="diff-line-num new_line" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2121

</td>

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

<pre style="margin: 0;"> <span id="LC2121" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2122

</td>

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

<pre style="margin: 0;">+<span id="LC2122" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">// if any</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2099

</td>

<td class="diff-line-num new_line" data-linenumber="2123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2123

</td>

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

<pre style="margin: 0;"> <span id="LC2123" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">LP</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">LP</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2100

</td>

<td class="diff-line-num new_line" data-linenumber="2124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2124

</td>

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

<pre style="margin: 0;"> <span id="LC2124" class="line" lang="cpp">                         <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="2101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2125

</td>

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

<pre style="margin: 0;">+<span id="LC2125" class="line" lang="cpp">                                 <span class="c1" style="color: #998; font-style: italic;">// look for maximum weight</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="2101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2101

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2126

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<pre style="margin: 0;"> <span id="LC2126" class="line" lang="cpp">                                 <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2102

</td>

<td class="diff-line-num new_line" data-linenumber="2127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2127

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<pre style="margin: 0;"> <span id="LC2127" class="line" lang="cpp">                                 <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">maxi</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2103

</td>

<td class="diff-line-num new_line" data-linenumber="2128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2128

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<pre style="margin: 0;"> <span id="LC2128" class="line" lang="cpp">                                 <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</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;">LP</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">LP</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2123" style="width: 35px; color: rgba(0,0,0,0.3); 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="2148" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2123,6 +2148,7 @@ std::vector<ConsensusPart> handleConsensus(</td>

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<td class="diff-line-num old_line" data-linenumber="2123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2123

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<td class="diff-line-num new_line" data-linenumber="2148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2148

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<pre style="margin: 0;"> <span id="LC2148" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                      std::cerr << "full path" << std::endl;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2124

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<td class="diff-line-num new_line" data-linenumber="2149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2149

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<pre style="margin: 0;"> <span id="LC2149" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                      #endif</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2125

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<td class="diff-line-num new_line" data-linenumber="2150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2150

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<pre style="margin: 0;"> <span id="LC2150" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2126" style="width: 35px; color: rgba(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="2151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2151

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<pre style="margin: 0;">+<span id="LC2151" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// decode kmer path</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2126

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<td class="diff-line-num new_line" data-linenumber="2152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2152

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<pre style="margin: 0;"> <span id="LC2152" class="line" lang="cpp">                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">fullpathstr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2127

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<td class="diff-line-num new_line" data-linenumber="2153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2153

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<pre style="margin: 0;"> <span id="LC2153" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">VBLmax</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2128

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<td class="diff-line-num new_line" data-linenumber="2154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2154

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<pre style="margin: 0;"> <span id="LC2154" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

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<br>

</li>

<li id="309ee1cabd82915dbfa35666ebc065bfb115dbac">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#309ee1cabd82915dbfa35666ebc065bfb115dbac"><strong>src/programs/bamfeaturecount.cpp</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,6 +137,8 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)</td>

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137

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp">  <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gtf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GTFData</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">pGTF</span><span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gtf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GTFData</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">obtain</span><span class="p">(</span><span class="n" style="color: #333;">annofn</span><span class="p">,</span><span class="n" style="color: #333;">verbose</span><span class="p">));</span></span>

</pre>

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138

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp">  <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gtf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GTFData</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gtfdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pGTF</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="140" style="width: 35px; color: rgba(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="140" style="width: 35px; color: rgba(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="LC140" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// gtfdata.print(std::cerr);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="140" style="width: 35px; color: rgba(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="141" style="width: 35px; color: rgba(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="LC141" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC142" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">exportcdna</span> <span class="p">)</span></span>

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141

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143

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp">  <span class="p">{</span></span>

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144

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp">          <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;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">hasArg</span><span class="p">(</span><span class="s" style="color: #d14;">"reference"</span><span class="p">)</span> <span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); 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="653" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -651,6 +653,10 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)</td>

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651

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653

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                                       }</span></span>

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652

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654

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<pre style="margin: 0;"> <span id="LC654" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                                       #endif</span></span>

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653

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655

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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp">                          <span class="p">}</span></span>

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656

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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">else</span></span>

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657

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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp">                          <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC658" class="line" lang="cpp">                                  <span class="c1" style="color: #998; font-style: italic;">// std::cerr << "[W] no GTF data found for " << algn.formatAlignment(bamheader) << std::endl;</span></span>

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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp">                          <span class="p">}</span></span>

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654

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<pre style="margin: 0;"> <span id="LC660" class="line" lang="cpp">                  <span class="p">}</span></span>

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661

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="cpp">                  <span class="c" style="color: #998; font-style: italic;">#if 0</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -672,7 +678,6 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)</td>

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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC679" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC680" class="line" lang="cpp">  <span class="p">{</span></span>

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675

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<td class="diff-line-num new_line old" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC675" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;"> <span id="LC681" class="line" lang="cpp">          <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">autoarray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AutoArray</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gtf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ExonInfo</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">AEI</span><span class="p">(</span><span class="n" style="color: #333;">gtfdata</span><span class="p">.</span><span class="n" style="color: #333;">Aexon</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

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682

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<pre style="margin: 0;"> <span id="LC682" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC683" class="line" lang="cpp">          <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sorting</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SerialisingSortingBufferedOutputFileArray</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gtf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ExonInterval</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">merger_ptr_type</span> <span class="n" style="color: #333;">merger</span><span class="p">(</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); 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="700" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -695,9 +700,10 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)</td>

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<pre style="margin: 0;"> <span id="LC700" class="line" lang="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">uncovered</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC701" class="line" lang="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">basecover</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC702" class="line" lang="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">total</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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="LC703" class="line" lang="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">maxdepth</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC704" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC705" class="line" lang="cpp">                          <span class="n" style="color: #333;">DepthCallback</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC700" class="line" lang="cpp">                          <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">uncovered</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">basecover</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">total</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="701" style="width: 35px; color: rgba(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="LC706" class="line" lang="cpp">                          <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">uncovered</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">basecover</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">total</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxdepth</span></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 right">)</span></span> <span class="p">{}</span></span>

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<td class="diff-line-num new_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC707" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC708" class="line" lang="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">from</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">depth</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC709" class="line" lang="cpp">                          <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); 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="711" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -705,6 +711,9 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)</td>

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<td class="diff-line-num new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC711" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="cpp">                                  <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">from</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC713" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="714" style="width: 35px; color: rgba(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="LC714" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxdepth</span> <span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

715

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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp">                                          <span class="n" style="color: #333;">maxdepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">depth</span><span class="p">;</span></span>

</pre>

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716

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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"></span>

</pre>

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708

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<td class="diff-line-num new_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

717

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<pre style="margin: 0;"> <span id="LC717" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">depth</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<td class="diff-line-num new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

718

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<pre style="margin: 0;"> <span id="LC718" class="line" lang="cpp">                                  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

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<td class="diff-line-num new_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

719

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<pre style="margin: 0;"> <span id="LC719" class="line" lang="cpp">                                          <span class="n" style="color: #333;">basecover</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">depth</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -841,13 +850,14 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)</td>

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841

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<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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<pre style="margin: 0;"> <span id="LC850" class="line" lang="cpp">                                          <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">unique</span><span class="p">.</span><span class="n" style="color: #333;">uncovered</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">DC</span><span class="p">.</span><span class="n" style="color: #333;">uncovered</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

842

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<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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<pre style="margin: 0;"> <span id="LC851" class="line" lang="cpp">                                          <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">unique</span><span class="p">.</span><span class="n" style="color: #333;">basecount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">DC</span><span class="p">.</span><span class="n" style="color: #333;">basecover</span><span class="p">;</span></span>

</pre>

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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

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<td class="diff-line-num new_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

852

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<pre style="margin: 0;"> <span id="LC852" class="line" lang="cpp">                                          <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">unique</span><span class="p">.</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">DC</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="844" style="width: 35px; color: rgba(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="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

853

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<pre style="margin: 0;">+<span id="LC853" class="line" lang="cpp">                                          <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">unique</span><span class="p">.</span><span class="n" style="color: #333;">maxdepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</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;">info</span><span class="p">.</span><span class="n" style="color: #333;">unique</span><span class="p">.</span><span class="n" style="color: #333;">maxdepth</span><span class="p">,</span><span class="n" style="color: #333;">DC</span><span class="p">.</span><span class="n" style="color: #333;">maxdepth</span><span class="p">);</span></span>

</pre>

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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

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<td class="diff-line-num new_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

854

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<pre style="margin: 0;"> <span id="LC854" class="line" lang="cpp">                                  <span class="p">}</span></span>

</pre>

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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

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<td class="diff-line-num new_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

855

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<pre style="margin: 0;"> <span id="LC855" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old_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="diff-line-num new_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

856

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

<pre style="margin: 0;"> <span id="LC856" class="line" lang="cpp">                                  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_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="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC857" class="line" lang="cpp">                                          <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">ambig</span><span class="p">.</span><span class="n" style="color: #333;">uncovered</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">DC</span><span class="p">.</span><span class="n" style="color: #333;">uncovered</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

848

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC858" class="line" lang="cpp">                                          <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">ambig</span><span class="p">.</span><span class="n" style="color: #333;">basecount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">DC</span><span class="p">.</span><span class="n" style="color: #333;">basecover</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC859" class="line" lang="cpp">                                          <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">ambig</span><span class="p">.</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">DC</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

850

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<td class="diff-line-num new_line old" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC850" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

860

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<pre style="margin: 0;">+<span id="LC860" class="line" lang="cpp">                                          <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">ambig</span><span class="p">.</span><span class="n" style="color: #333;">maxdepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</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;">info</span><span class="p">.</span><span class="n" style="color: #333;">ambig</span><span class="p">.</span><span class="n" style="color: #333;">maxdepth</span><span class="p">,</span><span class="n" style="color: #333;">DC</span><span class="p">.</span><span class="n" style="color: #333;">maxdepth</span><span class="p">);</span></span>

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<td class="diff-line-num old_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="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC861" class="line" lang="cpp">                                  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

852

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<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="cpp">                          <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

853

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<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

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<pre style="margin: 0;"> <span id="LC863" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); 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="912" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -902,8 +912,7 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)</td>

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<td class="diff-line-num old_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

902

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<td class="diff-line-num new_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

912

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<pre style="margin: 0;"> <span id="LC912" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtfdata</span><span class="p">.</span><span class="n" style="color: #333;">Aid</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">G</span><span class="p">.</span><span class="n" style="color: #333;">name_offset</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

903

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC913" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">o</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="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

904

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC914" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

905

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<td class="diff-line-num new_line old" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC905" class="line" lang="cpp">                  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">refidname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bamheader</span><span class="p">.</span><span class="n" style="color: #333;">getRefIDName</span><span class="p">(</span><span class="n" style="color: #333;">G</span><span class="p">.</span><span class="n" style="color: #333;">chr_id</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

906

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<td class="diff-line-num new_line old" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC906" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="907" style="width: 35px; color: rgba(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="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

915

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<pre style="margin: 0;">+<span id="LC915" class="line" lang="cpp">                  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">refidname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtfdata</span><span class="p">.</span><span class="n" style="color: #333;">Vchr</span><span class="p">[</span><span class="n" style="color: #333;">G</span><span class="p">.</span><span class="n" style="color: #333;">chr_id</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">//bamheader.getRefIDName(G.chr_id);</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="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

916

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<pre style="margin: 0;"> <span id="LC916" class="line" lang="cpp"></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="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

917

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<pre style="margin: 0;"> <span id="LC917" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">G</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ti</span> <span class="p">)</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="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

918

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<pre style="margin: 0;"> <span id="LC918" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>

</pre>

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<br>

</li>

<li id="2bcca0119361ca8be7efd810c71e6bb649b2407e">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#2bcca0119361ca8be7efd810c71e6bb649b2407e"><strong>src/programs/bamfilterk.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); 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="451" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -451,13 +451,14 @@ int bamfilterk(libmaus2::util::ArgInfo const & arginfo)</td>

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<td class="diff-line-num old_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

451

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<td class="diff-line-num new_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

451

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

452

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<td class="diff-line-num new_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

452

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">kmer</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">z</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC453" class="line" lang="cpp">                  <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp">                          <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "kmer " << kmer << " seqid " << seqid << " pos " << pos << " z " << z << std::endl;</span></span>

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp">                          <span class="n" style="color: #333;">AK</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">o_AK</span><span class="p">,</span><span class="n" style="color: #333;">KMer</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">,</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">z</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp">                  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp">          <span class="p">};</span></span>

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

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="cpp">          <span class="n" style="color: #333;">Callback</span> <span class="n" style="color: #333;">CB</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">AK</span><span class="p">,</span><span class="n" style="color: #333;">o_AK</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC460" class="line" lang="cpp">          <span class="n" style="color: #333;">KB</span><span class="p">.</span><span class="n" style="color: #333;">kmerCallbackPos</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp">          <span class="n" style="color: #333;">KB</span><span class="p">.</span><span class="n" style="color: #333;">kmerCallbackPos<span class="idiff left right">FR</span></span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp">                  <span class="n" style="color: #333;">Vref</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span></span>

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<pre style="margin: 0;"> <span id="LC463" class="line" lang="cpp">                  <span class="n" style="color: #333;">Vref</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">(),</span></span>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="cpp">                  <span class="n" style="color: #333;">CB</span><span class="p">,</span></span>

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<br>

</li>

<li id="12a6e0f37844ed1aef4085c8accc31117da2a7a3">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#12a6e0f37844ed1aef4085c8accc31117da2a7a3"><strong>src/programs/bamtofastq.1</strong></a>

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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>

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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">@@ -204,6 +204,10 @@ The suffixes k, m, g, K, M and G can be used to denote that the argument is</td>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="plaintext">to be multiplied by 1024, 1024^2, 1024^3, 1000, 1000^2 or 1000^3</span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext">respectively.</span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext">.PP</span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">.B cols=<>:</span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">If set to an unsigned number then wrap the sequence and quality lines at</span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">this number of columns. By default no wrapping is performed.</span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">.PP</span>

</pre>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext">.B splitprefix=<bamtofastq_split>:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext">file prefix if split>0 and collate=0.</span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">.PP</span>

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<br>

</li>

<li id="be752f41aab032268ccb172abc929cf063a40400">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#be752f41aab032268ccb172abc929cf063a40400"><strong>src/programs/bamtofastq.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -229,6 +229,11 @@ static uint64_t getDefaultMaxOutput()</td>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="nf" style="color: #900; font-weight: 600;">getDefaultCols</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp">  <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="LC235" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bamtofastq_conversion_type</span> <span class="n" style="color: #333;">conversion_type</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">bamtofastqNonCollating</span><span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgInfo</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arginfo</span><span class="p">,</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoder</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bamdec</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"><span class="p">{</span></span>

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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="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">...</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 +244,7 @@ void bamtofastqNonCollating(libmaus2::util::ArgInfo const & arginfo, libmaus2::b</td>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">gz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"gz"</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">split</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValueUnsignedNumeric</span><span class="p">(</span><span class="s" style="color: #d14;">"split"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultSplit</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">maxoutput</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValueUnsignedNumeric</span><span class="p">(</span><span class="s" style="color: #d14;">"maxoutput"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultMaxOutput</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValueUnsignedNumeric</span><span class="p">(</span><span class="s" style="color: #d14;">"cols"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultCols</span><span class="p">());</span></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">

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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="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">splitprefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getUnparsedValue</span><span class="p">(</span><span class="s" style="color: #d14;">"splitprefix"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultSplitPrefix</span><span class="p">());</span></span>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamBlockWriterBaseFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">checkCompressionLevel</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"level"</span><span class="p">,</span><span class="n" style="color: #333;">Z_DEFAULT_COMPRESSION</span><span class="p">));</span></span>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">excludeflags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamFlagBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringToFlags</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"exclude"</span><span class="p">,</span><span class="s" style="color: #d14;">"SECONDARY,SUPPLEMENTARY"</span><span class="p">));</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -256,6 +262,14 @@ void bamtofastqNonCollating(libmaus2::util::ArgInfo const & arginfo, libmaus2::b</td>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Vtags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseTags</span><span class="p">(</span><span class="n" style="color: #333;">s_auxtags</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp">  <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAuxFilterVector</span> <span class="n" style="color: #333;">auxtags</span><span class="p">(</span><span class="n" style="color: #333;">Vtags</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"></span>

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<td class="diff-line-num new old_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="LC265" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">cols</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;">1</span> <span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(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="LC266" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(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="LC267" class="line" lang="cpp">          <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LibMausException</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp">          <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">getStream</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[E] uneven numbers ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") for cols are not supported"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">          <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">split</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp">  <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mult</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSplitMultiplier</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">conversion_type</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -298,19 +312,19 @@ void bamtofastqNonCollating(libmaus2::util::ArgInfo const & arginfo, libmaus2::b</td>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp">                  <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="cpp">                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">D</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp">                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">D</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC316" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</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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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="cpp">                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">D</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">blocksize</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(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="LC318" class="line" lang="cpp">                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">D</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">blocksize</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp">                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">D</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="321" style="width: 35px; color: rgba(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="LC321" class="line" lang="cpp">                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">D</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="cpp">                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">D</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">blocksize</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp">                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">D</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">blocksize</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC326" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line old" 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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<pre style="margin: 0;">-<span id="LC313" class="line" lang="cpp">                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">D</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">blocksize</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp">                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">D</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">algn</span><span class="p">.</span><span class="n" style="color: #333;">blocksize</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp">                  <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC330" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); 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="451" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -437,6 +451,15 @@ void bamtofastqCollating(</td>

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451

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp">  <span class="n" style="color: #333;">CollateCombs</span> <span class="n" style="color: #333;">combs</span><span class="p">;</span></span>

</pre>

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438

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452

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"></span>

</pre>

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439

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">outputperreadgroup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="o" style="font-weight: 600;"><</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="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"outputperreadgroup"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultOutputPerReadgroup</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValueUnsignedNumeric</span><span class="p">(</span><span class="s" style="color: #d14;">"cols"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultCols</span><span class="p">());</span></span>

</pre>

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455

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

456

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">cols</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;">1</span> <span class="p">)</span></span>

</pre>

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457

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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458

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp">          <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LibMausException</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_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">

459

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp">          <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">getStream</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[E] uneven numbers ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") for cols are not supported"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp">          <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="461" style="width: 35px; color: rgba(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="LC461" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="462" style="width: 35px; color: rgba(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="LC462" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC463" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC464" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">s_auxtags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getUnparsedValue</span><span class="p">(</span><span class="s" style="color: #d14;">"tags"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultTags</span><span class="p">());</span></span>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Vtags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseTags</span><span class="p">(</span><span class="n" style="color: #333;">s_auxtags</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); 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="634" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -611,19 +634,19 @@ void bamtofastqCollating(</td>

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611

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<pre style="margin: 0;"> <span id="LC634" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC635" class="line" lang="cpp">                          <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

613

</td>

<td class="diff-line-num new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

636

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<pre style="margin: 0;"> <span id="LC636" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

614

</td>

<td class="diff-line-num new_line old" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC614" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

637

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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="LC637" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

615

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<td class="diff-line-num new_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

638

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="cpp">                                          <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="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

616

</td>

<td class="diff-line-num new_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

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

<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</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="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

617

</td>

<td class="diff-line-num new_line old" data-linenumber="640" style="width: 35px; color: rgba(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="LC617" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</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="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

640

</td>

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

<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

618

</td>

<td class="diff-line-num new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

641

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

<pre style="margin: 0;"> <span id="LC641" class="line" lang="cpp">                                          <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="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

619

</td>

<td class="diff-line-num new_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

642

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

<pre style="margin: 0;"> <span id="LC642" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</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="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

620

</td>

<td class="diff-line-num new_line old" data-linenumber="643" style="width: 35px; color: rgba(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="LC620" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

643

</td>

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

<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

</td>

<td class="diff-line-num new_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

644

</td>

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

<pre style="margin: 0;"> <span id="LC644" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">break</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="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

</td>

<td class="diff-line-num new_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

645

</td>

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

<pre style="margin: 0;"> <span id="LC645" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</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="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

623

</td>

<td class="diff-line-num new_line old" data-linenumber="646" style="width: 35px; color: rgba(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="LC623" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

646

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<pre style="margin: 0;">+<span id="LC646" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

624

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<td class="diff-line-num new_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

647

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<pre style="margin: 0;"> <span id="LC647" class="line" lang="cpp">                                          <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="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

625

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<td class="diff-line-num new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

648

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<pre style="margin: 0;"> <span id="LC648" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

626

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<td class="diff-line-num new_line old" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC626" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="627" style="width: 35px; color: rgba(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="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

649

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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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627

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<td class="diff-line-num new_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

650

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<pre style="margin: 0;"> <span id="LC650" class="line" lang="cpp">                                          <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="628" style="width: 35px; color: rgba(0,0,0,0.3); 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="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

651

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp">                          <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); 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="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

652

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); 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="657" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -634,19 +657,19 @@ void bamtofastqCollating(</td>

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657

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

635

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<td class="diff-line-num new_line" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

658

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="cpp">                          <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); 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="659" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC659" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

637

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<td class="diff-line-num new_line old" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC637" class="line" lang="cpp">                                          <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="638" style="width: 35px; color: rgba(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="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

660

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<pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp">                                          <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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638

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<td class="diff-line-num new_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

661

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="cpp">                                          <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="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

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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="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

640

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<td class="diff-line-num new_line old" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC640" class="line" lang="cpp">                                          <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

663

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp">                                          <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

641

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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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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cpp">                                          <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="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

642

</td>

<td class="diff-line-num new_line" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

665

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

<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

643

</td>

<td class="diff-line-num new_line old" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC643" class="line" lang="cpp">                                          <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

666

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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="LC666" class="line" lang="cpp">                                          <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

644

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<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

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

<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp">                                          <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="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

645

</td>

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

<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

646

</td>

<td class="diff-line-num new_line old" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC646" class="line" lang="cpp">                                          <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

669

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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="LC669" class="line" lang="cpp">                                          <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

647

</td>

<td class="diff-line-num new_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

670

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

<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

648

</td>

<td class="diff-line-num new_line" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

671

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

<pre style="margin: 0;"> <span id="LC671" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

649

</td>

<td class="diff-line-num new_line old" data-linenumber="672" style="width: 35px; color: rgba(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="LC649" class="line" lang="cpp">                                          <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</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="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

672

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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="LC672" class="line" lang="cpp">                                          <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC673" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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651

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674

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<pre style="margin: 0;"> <span id="LC674" class="line" lang="cpp">                          <span class="p">}</span></span>

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675

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -663,19 +686,19 @@ void bamtofastqCollating(</td>

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<pre style="margin: 0;"> <span id="LC686" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC687" class="line" lang="cpp">                          <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC688" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC666" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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690

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<pre style="margin: 0;"> <span id="LC690" class="line" lang="cpp">                                          <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_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

691

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<pre style="margin: 0;"> <span id="LC691" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC669" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

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692

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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC693" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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671

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<td class="diff-line-num new_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

694

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<pre style="margin: 0;"> <span id="LC694" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</span><span class="p">:</span></span>

</pre>

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672

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<td class="diff-line-num new_line old" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC672" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

673

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<td class="diff-line-num new_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

696

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<pre style="margin: 0;"> <span id="LC696" class="line" lang="cpp">                                          <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="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

674

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<td class="diff-line-num new_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

697

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<pre style="margin: 0;"> <span id="LC697" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

675

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<td class="diff-line-num new_line old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC675" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="676" style="width: 35px; color: rgba(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="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

698

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

676

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<td class="diff-line-num new_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

699

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<pre style="margin: 0;"> <span id="LC699" class="line" lang="cpp">                                          <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="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">

677

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<td class="diff-line-num new_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

700

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<pre style="margin: 0;"> <span id="LC700" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

678

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<td class="diff-line-num new_line old" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC678" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="679" style="width: 35px; color: rgba(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="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

701

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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></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="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

702

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<pre style="margin: 0;"> <span id="LC702" class="line" lang="cpp">                                          <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="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

680

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<td class="diff-line-num new_line" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

703

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<pre style="margin: 0;"> <span id="LC703" class="line" lang="cpp">                          <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

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<td class="diff-line-num new_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

704

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<pre style="margin: 0;"> <span id="LC704" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); 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="715" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -692,19 +715,19 @@ void bamtofastqCollating(</td>

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<td class="diff-line-num old_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

692

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<td class="diff-line-num new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

693

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<td class="diff-line-num new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp">                          <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

694

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<td class="diff-line-num new_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

717

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<pre style="margin: 0;"> <span id="LC717" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

695

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<td class="diff-line-num new_line old" data-linenumber="718" style="width: 35px; color: rgba(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="LC695" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</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="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

718

</td>

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

<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

696

</td>

<td class="diff-line-num new_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

719

</td>

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

<pre style="margin: 0;"> <span id="LC719" class="line" lang="cpp">                                          <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="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

697

</td>

<td class="diff-line-num new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

720

</td>

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

<pre style="margin: 0;"> <span id="LC720" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</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="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

698

</td>

<td class="diff-line-num new_line old" data-linenumber="721" style="width: 35px; color: rgba(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="LC698" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</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="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

721

</td>

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

<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

699

</td>

<td class="diff-line-num new_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

</td>

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

<pre style="margin: 0;"> <span id="LC722" class="line" lang="cpp">                                          <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="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

700

</td>

<td class="diff-line-num new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

723

</td>

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

<pre style="margin: 0;"> <span id="LC723" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</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="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

701

</td>

<td class="diff-line-num new_line old" data-linenumber="724" style="width: 35px; color: rgba(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="LC701" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

724

</td>

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

<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

702

</td>

<td class="diff-line-num new_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

</td>

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

<pre style="margin: 0;"> <span id="LC725" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">break</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="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

703

</td>

<td class="diff-line-num new_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

</td>

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

<pre style="margin: 0;"> <span id="LC726" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</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="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

704

</td>

<td class="diff-line-num new_line old" data-linenumber="727" style="width: 35px; color: rgba(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="LC704" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

727

</td>

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

<pre style="margin: 0;">+<span id="LC727" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

</td>

<td class="diff-line-num new_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

728

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<pre style="margin: 0;"> <span id="LC728" class="line" lang="cpp">                                          <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="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

706

</td>

<td class="diff-line-num new_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

729

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

<pre style="margin: 0;"> <span id="LC729" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

707

</td>

<td class="diff-line-num new_line old" data-linenumber="730" style="width: 35px; color: rgba(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="LC707" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

730

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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="LC730" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

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<td class="diff-line-num new_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

731

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<pre style="margin: 0;"> <span id="LC731" class="line" lang="cpp">                                          <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="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<td class="diff-line-num new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

732

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<pre style="margin: 0;"> <span id="LC732" class="line" lang="cpp">                          <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

</td>

<td class="diff-line-num new_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

733

</td>

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

<pre style="margin: 0;"> <span id="LC733" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); 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="744" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -721,19 +744,19 @@ void bamtofastqCollating(</td>

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<td class="diff-line-num old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

721

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<td class="diff-line-num new_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

744

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<pre style="margin: 0;"> <span id="LC744" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

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<td class="diff-line-num new_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

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<pre style="margin: 0;"> <span id="LC745" class="line" lang="cpp">                          <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

723

</td>

<td class="diff-line-num new_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

746

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

<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

724

</td>

<td class="diff-line-num new_line old" data-linenumber="747" style="width: 35px; color: rgba(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="LC724" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</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="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

747

</td>

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

<pre style="margin: 0;">+<span id="LC747" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

</td>

<td class="diff-line-num new_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

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

<pre style="margin: 0;"> <span id="LC748" class="line" lang="cpp">                                          <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="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

</td>

<td class="diff-line-num new_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

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

<pre style="margin: 0;"> <span id="LC749" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</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="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

727

</td>

<td class="diff-line-num new_line old" data-linenumber="750" style="width: 35px; color: rgba(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="LC727" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

750

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<pre style="margin: 0;">+<span id="LC750" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

728

</td>

<td class="diff-line-num new_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

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

<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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

<td class="diff-line-num old_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

729

</td>

<td class="diff-line-num new_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

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

<pre style="margin: 0;"> <span id="LC752" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</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="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

730

</td>

<td class="diff-line-num new_line old" data-linenumber="753" style="width: 35px; color: rgba(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="LC730" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

753

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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="LC753" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

731

</td>

<td class="diff-line-num new_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

754

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

<pre style="margin: 0;"> <span id="LC754" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

732

</td>

<td class="diff-line-num new_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

755

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

<pre style="margin: 0;"> <span id="LC755" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</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="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

733

</td>

<td class="diff-line-num new_line old" data-linenumber="756" style="width: 35px; color: rgba(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="LC733" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

756

</td>

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

<pre style="margin: 0;">+<span id="LC756" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

</td>

<td class="diff-line-num new_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

</td>

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

<pre style="margin: 0;"> <span id="LC757" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">break</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="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

735

</td>

<td class="diff-line-num new_line" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

758

</td>

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

<pre style="margin: 0;"> <span id="LC758" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</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="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

736

</td>

<td class="diff-line-num new_line old" data-linenumber="759" style="width: 35px; color: rgba(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="LC736" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</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="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

759

</td>

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

<pre style="margin: 0;">+<span id="LC759" class="line" lang="cpp">                                          <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

</td>

<td class="diff-line-num new_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

760

</td>

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

<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp">                                          <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="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

738

</td>

<td class="diff-line-num new_line" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

761

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

<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp">                          <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

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<td class="diff-line-num new_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

762

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<pre style="margin: 0;"> <span id="LC762" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -796,19 +819,19 @@ void bamtofastqCollating(</td>

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<td class="diff-line-num old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

796

</td>

<td class="diff-line-num new_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

819

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

<pre style="margin: 0;"> <span id="LC819" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

</td>

<td class="diff-line-num new_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

820

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<pre style="margin: 0;"> <span id="LC820" class="line" lang="cpp">                                  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

798

</td>

<td class="diff-line-num new_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

821

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

<pre style="margin: 0;"> <span id="LC821" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

799

</td>

<td class="diff-line-num new_line old" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC799" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</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="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

822

</td>

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

<pre style="margin: 0;">+<span id="LC822" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

800

</td>

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

<pre style="margin: 0;"> <span id="LC823" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

801

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC824" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</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="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

802

</td>

<td class="diff-line-num new_line old" data-linenumber="825" style="width: 35px; color: rgba(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="LC802" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</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="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

825

</td>

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

<pre style="margin: 0;">+<span id="LC825" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

803

</td>

<td class="diff-line-num new_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

</td>

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

<pre style="margin: 0;"> <span id="LC826" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

804

</td>

<td class="diff-line-num new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

827

</td>

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

<pre style="margin: 0;"> <span id="LC827" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</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="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

805

</td>

<td class="diff-line-num new_line old" data-linenumber="828" style="width: 35px; color: rgba(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="LC805" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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

</td>

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

<pre style="margin: 0;">+<span id="LC828" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

806

</td>

<td class="diff-line-num new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

829

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<pre style="margin: 0;"> <span id="LC829" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

807

</td>

<td class="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC830" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

808

</td>

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

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<pre style="margin: 0;">-<span id="LC808" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC831" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

809

</td>

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

<pre style="margin: 0;"> <span id="LC832" class="line" lang="cpp">                                                  <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="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

810

</td>

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

<pre style="margin: 0;"> <span id="LC833" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

811

</td>

<td class="diff-line-num new_line old" data-linenumber="834" style="width: 35px; color: rgba(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="LC811" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</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="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

834

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

<pre style="margin: 0;">+<span id="LC834" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

812

</td>

<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

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<pre style="margin: 0;"> <span id="LC835" class="line" lang="cpp">                                                  <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="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

813

</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

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

<pre style="margin: 0;"> <span id="LC836" class="line" lang="cpp">                                  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

814

</td>

<td class="diff-line-num new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

837

</td>

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

<pre style="margin: 0;"> <span id="LC837" class="line" lang="cpp">                                  <span class="n" style="color: #333;">OFS</span><span class="p">.</span><span class="n" style="color: #333;">Fout</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">la</span><span class="p">);</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -817,19 +840,19 @@ void bamtofastqCollating(</td>

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<td class="diff-line-num old_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

817

</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

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<pre style="margin: 0;"> <span id="LC840" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

818

</td>

<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC841" class="line" lang="cpp">                                  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

819

</td>

<td class="diff-line-num new_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

842

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

<pre style="margin: 0;"> <span id="LC842" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

820

</td>

<td class="diff-line-num new_line old" data-linenumber="843" style="width: 35px; color: rgba(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="LC820" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_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">

843

</td>

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

<pre style="margin: 0;">+<span id="LC843" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

821

</td>

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

<pre style="margin: 0;"> <span id="LC844" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</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="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

822

</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

</td>

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

<pre style="margin: 0;"> <span id="LC845" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</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="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

823

</td>

<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(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="LC823" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">T</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="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

846

</td>

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

<pre style="margin: 0;">+<span id="LC846" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="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

</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

</td>

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

<pre style="margin: 0;"> <span id="LC847" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</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="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

</td>

<td class="diff-line-num new_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

848

</td>

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

<pre style="margin: 0;"> <span id="LC848" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</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="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

826

</td>

<td class="diff-line-num new_line old" data-linenumber="849" style="width: 35px; color: rgba(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="LC826" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">T</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

849

</td>

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

<pre style="margin: 0;">+<span id="LC849" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="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

</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

</td>

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

<pre style="margin: 0;"> <span id="LC850" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</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="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

828

</td>

<td class="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

</td>

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

<pre style="margin: 0;"> <span id="LC851" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</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="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

829

</td>

<td class="diff-line-num new_line old" data-linenumber="852" style="width: 35px; color: rgba(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="LC829" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">T</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

852

</td>

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

<pre style="margin: 0;">+<span id="LC852" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="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="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

853

</td>

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

<pre style="margin: 0;"> <span id="LC853" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</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="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

831

</td>

<td class="diff-line-num new_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

854

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<pre style="margin: 0;"> <span id="LC854" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

832

</td>

<td class="diff-line-num new_line old" data-linenumber="855" style="width: 35px; color: rgba(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="LC832" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

855

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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="LC855" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

856

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<pre style="margin: 0;"> <span id="LC856" class="line" lang="cpp">                                                  <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="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="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

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<pre style="margin: 0;"> <span id="LC857" class="line" lang="cpp">                                  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_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>

<td class="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC858" class="line" lang="cpp">                                  <span class="n" style="color: #333;">OFS</span><span class="p">.</span><span class="n" style="color: #333;">F2out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">lb</span><span class="p">);</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -844,19 +867,19 @@ void bamtofastqCollating(</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

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<td class="diff-line-num new_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

867

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<pre style="margin: 0;"> <span id="LC867" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

</pre>

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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

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<td class="diff-line-num new_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

868

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<pre style="margin: 0;"> <span id="LC868" class="line" lang="cpp">                                  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_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="diff-line-num new_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

869

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

<pre style="margin: 0;"> <span id="LC869" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

847

</td>

<td class="diff-line-num new_line old" data-linenumber="870" style="width: 35px; color: rgba(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="LC847" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_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">

</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

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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="LC870" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

848

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<td class="diff-line-num new_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

871

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<pre style="margin: 0;"> <span id="LC871" class="line" lang="cpp">                                                  <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="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

</td>

<td class="diff-line-num new_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

872

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

<pre style="margin: 0;"> <span id="LC872" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

850

</td>

<td class="diff-line-num new_line old" data-linenumber="873" style="width: 35px; color: rgba(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="LC850" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-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="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_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

</td>

<td class="diff-line-num new_line" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

874

</td>

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

<pre style="margin: 0;"> <span id="LC874" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

852

</td>

<td class="diff-line-num new_line" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

875

</td>

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

<pre style="margin: 0;"> <span id="LC875" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</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="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

853

</td>

<td class="diff-line-num new_line old" data-linenumber="876" style="width: 35px; color: rgba(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="LC853" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-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="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

854

</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

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

<pre style="margin: 0;"> <span id="LC877" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

855

</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="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</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="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

856

</td>

<td class="diff-line-num new_line old" data-linenumber="879" style="width: 35px; color: rgba(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="LC856" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

879

</td>

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

<pre style="margin: 0;">+<span id="LC879" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

880

</td>

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

<pre style="margin: 0;"> <span id="LC880" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</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="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="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

881

</td>

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

<pre style="margin: 0;"> <span id="LC881" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</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="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

859

</td>

<td class="diff-line-num new_line old" data-linenumber="882" style="width: 35px; color: rgba(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="LC859" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</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="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

882

</td>

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

<pre style="margin: 0;">+<span id="LC882" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="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="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

883

</td>

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

<pre style="margin: 0;"> <span id="LC883" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</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="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="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

884

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<pre style="margin: 0;"> <span id="LC884" class="line" lang="cpp">                                  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

885

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<pre style="margin: 0;"> <span id="LC885" class="line" lang="cpp">                                  <span class="n" style="color: #333;">OFS</span><span class="p">.</span><span class="n" style="color: #333;">Sout</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">la</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); 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="894" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -871,19 +894,19 @@ void bamtofastqCollating(</td>

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<td class="diff-line-num old_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

871

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<td class="diff-line-num new_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

894

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<pre style="margin: 0;"> <span id="LC894" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

872

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<td class="diff-line-num new_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

895

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<pre style="margin: 0;"> <span id="LC895" class="line" lang="cpp">                                  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

873

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<td class="diff-line-num new_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

896

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<pre style="margin: 0;"> <span id="LC896" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

874

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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC874" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

897

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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="LC897" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

875

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<td class="diff-line-num new_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

898

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<pre style="margin: 0;"> <span id="LC898" class="line" lang="cpp">                                                  <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="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

876

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<td class="diff-line-num new_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

899

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<pre style="margin: 0;"> <span id="LC899" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

877

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<td class="diff-line-num new_line old" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC877" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="878" style="width: 35px; color: rgba(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="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

900

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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="LC900" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_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

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<td class="diff-line-num new_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

901

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<pre style="margin: 0;"> <span id="LC901" class="line" lang="cpp">                                                  <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="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

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<td class="diff-line-num new_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

902

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<pre style="margin: 0;"> <span id="LC902" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

880

</td>

<td class="diff-line-num new_line old" data-linenumber="903" style="width: 35px; color: rgba(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="LC880" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="881" style="width: 35px; color: rgba(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="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

903

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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="LC903" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

881

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<td class="diff-line-num new_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

904

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<pre style="margin: 0;"> <span id="LC904" class="line" lang="cpp">                                                  <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="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

882

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<td class="diff-line-num new_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

905

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<pre style="margin: 0;"> <span id="LC905" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

883

</td>

<td class="diff-line-num new_line old" data-linenumber="906" style="width: 35px; color: rgba(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="LC883" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

906

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<pre style="margin: 0;">+<span id="LC906" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

884

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC907" class="line" lang="cpp">                                                  <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="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

885

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC908" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

886

</td>

<td class="diff-line-num new_line old" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC886" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="887" style="width: 35px; color: rgba(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="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">

909

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<pre style="margin: 0;">+<span id="LC909" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC910" class="line" lang="cpp">                                                  <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="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

888

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

<pre style="margin: 0;"> <span id="LC911" class="line" lang="cpp">                                  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

889

</td>

<td class="diff-line-num new_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

912

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

<pre style="margin: 0;"> <span id="LC912" class="line" lang="cpp">                                  <span class="n" style="color: #333;">OFS</span><span class="p">.</span><span class="n" style="color: #333;">Oout</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">la</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); 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="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -898,19 +921,19 @@ void bamtofastqCollating(</td>

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<td class="diff-line-num old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

898

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<td class="diff-line-num new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

921

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<pre style="margin: 0;"> <span id="LC921" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span> <span class="n" style="color: #333;">conversion_type</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

899

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<td class="diff-line-num new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

922

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<pre style="margin: 0;"> <span id="LC922" class="line" lang="cpp">                                  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

900

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<td class="diff-line-num new_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

923

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

<pre style="margin: 0;"> <span id="LC923" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fasta</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

901

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<td class="diff-line-num new_line old" data-linenumber="924" style="width: 35px; color: rgba(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="LC901" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</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="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

924

</td>

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

<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastA</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

902

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC925" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</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="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

903

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC926" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq</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="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

904

</td>

<td class="diff-line-num new_line old" data-linenumber="927" style="width: 35px; color: rgba(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="LC904" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</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="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-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

</td>

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

<pre style="margin: 0;">+<span id="LC927" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

905

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC928" class="line" lang="cpp">                                                  <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="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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_casava18</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="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

907

</td>

<td class="diff-line-num new_line old" data-linenumber="930" style="width: 35px; color: rgba(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="LC907" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

930

</td>

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

<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQCasava18</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="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

</td>

<td class="diff-line-num new_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

931

</td>

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

<pre style="margin: 0;"> <span id="LC931" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</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="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

</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

</td>

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

<pre style="margin: 0;"> <span id="LC932" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_try_oq</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="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

910

</td>

<td class="diff-line-num new_line old" data-linenumber="933" style="width: 35px; color: rgba(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="LC910" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</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="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

933

</td>

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

<pre style="margin: 0;">+<span id="LC933" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQTryOQ</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></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="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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC934" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</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="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

912

</td>

<td class="diff-line-num new_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

935

</td>

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

<pre style="margin: 0;"> <span id="LC935" class="line" lang="cpp">                                          <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bamtofastq_conversion_type_fastq_aux</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="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

913

</td>

<td class="diff-line-num new_line old" data-linenumber="936" style="width: 35px; color: rgba(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="LC913" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</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="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

936

</td>

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

<pre style="margin: 0;">+<span id="LC936" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQAux</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">,</span><span class="n" style="color: #333;">auxtags</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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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

</td>

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

<pre style="margin: 0;"> <span id="LC937" class="line" lang="cpp">                                                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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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

</td>

<td class="diff-line-num new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

938

</td>

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

<pre style="margin: 0;"> <span id="LC938" class="line" lang="cpp">                                  <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

916

</td>

<td class="diff-line-num new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

939

</td>

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

<pre style="margin: 0;"> <span id="LC939" class="line" lang="cpp">                                  <span class="n" style="color: #333;">OFS</span><span class="p">.</span><span class="n" style="color: #333;">O2out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">la</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="1037" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1037,6 +1060,15 @@ void bamtofastqCollatingRanking(</td>

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<td class="diff-line-num old_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1037

</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="cpp">         <span class="n" style="color: #333;">CHCBD</span><span class="p">.</span><span class="n" style="color: #333;">disableValidation</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="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1038

</td>

<td class="diff-line-num new_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1061

</td>

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

<pre style="margin: 0;"> <span id="LC1061" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1039

</td>

<td class="diff-line-num new_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1062

</td>

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

<pre style="margin: 0;"> <span id="LC1062" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamToFastqOutputFileSet</span> <span class="n" style="color: #333;">OFS</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1063

</td>

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

<pre style="margin: 0;">+<span id="LC1063" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValueUnsignedNumeric</span><span class="p">(</span><span class="s" style="color: #d14;">"cols"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultCols</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1064

</td>

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

<pre style="margin: 0;">+<span id="LC1064" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1065

</td>

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

<pre style="margin: 0;">+<span id="LC1065" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">cols</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;">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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1066

</td>

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

<pre style="margin: 0;">+<span id="LC1066" class="line" lang="cpp"> <span class="p">{</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1067

</td>

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

<pre style="margin: 0;">+<span id="LC1067" class="line" lang="cpp">         <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LibMausException</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1068

</td>

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

<pre style="margin: 0;">+<span id="LC1068" class="line" lang="cpp">         <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">getStream</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[E] uneven numbers ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") for cols are not supported"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1069

</td>

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

<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp">         <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1070

</td>

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

<pre style="margin: 0;">+<span id="LC1070" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1071

</td>

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

<pre style="margin: 0;">+<span id="LC1071" class="line" lang="cpp"> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1040

</td>

<td class="diff-line-num new_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1072

</td>

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

<pre style="margin: 0;"> <span id="LC1072" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_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="diff-line-num new_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1073

</td>

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

<pre style="margin: 0;"> <span id="LC1073" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span></span>

</pre>

</td>

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<td class="diff-line-num old_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="diff-line-num new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1074

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

<pre style="margin: 0;"> <span id="LC1074" class="line" lang="cpp"> <span class="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1059,9 +1091,9 @@ void bamtofastqCollatingRanking(</td>

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<td class="diff-line-num old_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

</td>

<td class="diff-line-num new_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1091

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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_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

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<td class="diff-line-num new_line" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1092

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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ranka</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getRank</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1061

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<td class="diff-line-num new_line" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1093

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<pre style="margin: 0;"> <span id="LC1093" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">rankb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getRank</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizeb</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1062

</td>

<td class="diff-line-num new_line old" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1062" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQRanks</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">rankb</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1094

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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="LC1094" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQRanks</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">rankb</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1063

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<td class="diff-line-num new_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1095

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

<pre style="margin: 0;"> <span id="LC1095" class="line" lang="cpp">                         <span class="n" style="color: #333;">OFS</span><span class="p">.</span><span class="n" style="color: #333;">Fout</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">la</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1064

</td>

<td class="diff-line-num new_line old" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1064" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQRanks</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">rankb</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1096

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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="LC1096" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">lb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQRanks</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Db</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">rankb</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1065

</td>

<td class="diff-line-num new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1097

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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="cpp">                         <span class="n" style="color: #333;">OFS</span><span class="p">.</span><span class="n" style="color: #333;">F2out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">lb</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1066

</td>

<td class="diff-line-num new_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1098

</td>

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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1067

</td>

<td class="diff-line-num new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1099

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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="cpp">                         <span class="n" style="color: #333;">combs</span><span class="p">.</span><span class="n" style="color: #333;">pairs</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 match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); 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="1104" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1072,7 +1104,7 @@ void bamtofastqCollatingRanking(</td>

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<td class="diff-line-num old_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1072

</td>

<td class="diff-line-num new_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1104

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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1073

</td>

<td class="diff-line-num new_line" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1105

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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ranka</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getRank</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1074

</td>

<td class="diff-line-num 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">

1106

</td>

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

<pre style="margin: 0;"> <span id="LC1106" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1075

</td>

<td class="diff-line-num new_line old" data-linenumber="1107" style="width: 35px; color: rgba(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="LC1075" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQRanks</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1107

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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="LC1107" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQRanks</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1076

</td>

<td class="diff-line-num new_line" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1108

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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="cpp">                         <span class="n" style="color: #333;">OFS</span><span class="p">.</span><span class="n" style="color: #333;">Sout</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">la</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1077

</td>

<td class="diff-line-num new_line" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1109

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

<pre style="margin: 0;"> <span id="LC1109" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1078

</td>

<td class="diff-line-num new_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1110

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

<pre style="margin: 0;"> <span id="LC1110" class="line" lang="cpp">                         <span class="n" style="color: #333;">combs</span><span class="p">.</span><span class="n" style="color: #333;">single</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 unfold js-unfold old_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); 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="1115" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1083,7 +1115,7 @@ void bamtofastqCollatingRanking(</td>

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<td class="diff-line-num old_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1083

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<td class="diff-line-num new_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1115

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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1084

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<td class="diff-line-num new_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1116

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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ranka</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getRank</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1085

</td>

<td class="diff-line-num new_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1117

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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1086

</td>

<td class="diff-line-num new_line old" data-linenumber="1118" style="width: 35px; color: rgba(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="LC1086" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQRanks</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1118

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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQRanks</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1087

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<td class="diff-line-num new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1119

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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="cpp">                         <span class="n" style="color: #333;">OFS</span><span class="p">.</span><span class="n" style="color: #333;">Oout</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">la</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1088

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<td class="diff-line-num new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1120

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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1089

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<td class="diff-line-num new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1121

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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="cpp">                         <span class="n" style="color: #333;">combs</span><span class="p">.</span><span class="n" style="color: #333;">orphans1</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="1094" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1094,7 +1126,7 @@ void bamtofastqCollatingRanking(</td>

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<td class="diff-line-num old_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1094

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1095

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC1127" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ranka</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getRank</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blocksizea</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1096

</td>

<td class="diff-line-num new_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1128

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

<pre style="margin: 0;"> <span id="LC1128" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1097

</td>

<td class="diff-line-num new_line old" data-linenumber="1129" style="width: 35px; color: rgba(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="LC1097" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQRanks</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">T</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="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_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">

1129

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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="LC1129" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">la</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">putFastQRanks</span><span class="p">(</span><span class="n" style="color: #333;">ob</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Da</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">ranka</span><span class="p">,</span><span class="n" style="color: #333;">T</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">cols</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1098

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<td class="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC1130" class="line" lang="cpp">                         <span class="n" style="color: #333;">OFS</span><span class="p">.</span><span class="n" style="color: #333;">O2out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">la</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1099

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1100

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<td class="diff-line-num new_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1132

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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="cpp">                         <span class="n" style="color: #333;">combs</span><span class="p">.</span><span class="n" style="color: #333;">orphans2</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="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1331" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1299,6 +1331,7 @@ int main(int argc, char * argv[])</td>

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<td class="diff-line-num new_line" data-linenumber="1331" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1331" class="line" lang="cpp">                         <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span> <span class="s" style="color: #d14;">"outputperreadgroupprefix=<[]>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"prefix added in front of file names if outputperreadgroup=1 (for collate=1 only)"</span> <span class="p">)</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1332

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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="cpp">                         <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"casava18=<["</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NumberSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">formatNumber</span><span class="p">(</span><span class="n" style="color: #333;">getDefaultCasava18</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="s" style="color: #d14;">"]>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restore input taken by c18pe option"</span> <span class="p">)</span> <span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="1333" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1333" class="line" lang="cpp">                         <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span> <span class="s" style="color: #d14;">"maxoutput=<[]>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"output no more than this number of entries (default: no limit, collate=0 only)"</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="1302" style="width: 35px; color: rgba(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="1334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1334

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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="cpp">                         <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span> <span class="s" style="color: #d14;">"cols=<[]>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"wrap sequence and quality lines at this number of columns (default: do not wrap, even numbers only)"</span> <span class="p">)</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1302

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<td class="diff-line-num new_line" data-linenumber="1335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1335

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<pre style="margin: 0;"> <span id="LC1335" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1303

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<td class="diff-line-num new_line" data-linenumber="1336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1336

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<pre style="margin: 0;"> <span id="LC1336" class="line" lang="cpp">                         <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">printMap</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span><span class="n" style="color: #333;">V</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); 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="1337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1337

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<pre style="margin: 0;"> <span id="LC1337" class="line" lang="cpp"></span>

</pre>

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<br>

</li>

<li id="b9286f7204613857b6b691786b51e7d8e88e6929">

<a href="https://salsa.debian.org/med-team/biobambam2/commit/fcb2ab68688ae1e6fb59c424684fa2567ad9a44a#b9286f7204613857b6b691786b51e7d8e88e6929"><strong>src/programs/vcfreplacecontigs.cpp</strong></a>

<hr>

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<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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</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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<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

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    bambam</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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<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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    Copyright (C) 2019 German Tischler</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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<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="cpp"></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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<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="cpp"><span class="cm" style="color: #998; font-style: italic;">    This program is free software: you can redistribute it and/or modify</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    it under the terms of the GNU General Public License as published by</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    the Free Software Foundation, either version 3 of the License, or</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    (at your option) any later version.</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    This program is distributed in the hope that it will be useful,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    GNU General Public License for more details.</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    You should have received a copy of the GNU General Public License</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    along with this program.  If not, see <http://www.gnu.org/licenses/>.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">**/</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <config.h></span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/vcf/VCFParser.hpp></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/lz/BgzfDeflate.hpp></span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/fastx/FastAReader.hpp></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <biobambam2/Licensing.hpp></span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getDefaultVerbose</span><span class="p">()</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 class="p">}</span></span>

</pre>

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

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">vcfreplacecontigs</span><span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgInfo</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arginfo</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</span><span class="p">)</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="p">{</span></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="cpp">   <span class="c1" style="color: #998; font-style: italic;">//unsigned int const verbose = arginfo.getValue<unsigned int>("verbose",getDefaultVerbose());</span></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="cpp">   <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">gz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"gz"</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 new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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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="cpp">   <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfOutputStream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">pBOS</span><span class="p">;</span></span>

</pre>

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<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">

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">gz</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(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="LC37" class="line" lang="cpp">   <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(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="LC38" class="line" lang="cpp">           <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfOutputStream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">tBOS</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfOutputStream</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">));</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp">           <span class="n" style="color: #333;">pBOS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UNIQUE_PTR_MOVE</span><span class="p">(</span><span class="n" style="color: #333;">tBOS</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_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="LC40" class="line" lang="cpp">   <span class="p">}</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp">   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">vout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gz</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pBOS</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"></span>

</pre>

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44

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp">   <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">VCFParser</span> <span class="n" style="color: #333;">vcf</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>

</pre>

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45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"></span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp">   <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="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getNumRestArgs</span><span class="p">()</span> <span class="p">)</span> <span class="p">)</span></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp">   <span class="p">{</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">           <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[E] usage: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">progname</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <in.fa> <in.vcf"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<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">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">   <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp">   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">fafn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getUnparsedRestArg</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 new_line" data-linenumber="53" style="width: 35px; color: rgba(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="LC53" class="line" lang="cpp">   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Chromosome</span><span class="o" style="font-weight: 600;">></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 new_line" data-linenumber="54" style="width: 35px; color: rgba(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="LC54" class="line" lang="cpp">   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">S</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(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="LC55" class="line" lang="cpp">   <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(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="LC56" class="line" lang="cpp">           <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fastx</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastAReader</span> <span class="n" style="color: #333;">FA</span><span class="p">(</span><span class="n" style="color: #333;">fafn</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(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="LC57" class="line" lang="cpp">           <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fastx</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastAReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pattern_type</span> <span class="n" style="color: #333;">pat</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(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="LC58" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">FA</span><span class="p">.</span><span class="n" style="color: #333;">getNextPatternUnlocked</span><span class="p">(</span><span class="n" style="color: #333;">pat</span><span class="p">)</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(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="LC59" class="line" lang="cpp">           <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp">                   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">getShortStringId</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp">                   <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Chromosome</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span><span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">spattern</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp">                   <span class="n" style="color: #333;">S</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp">                   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[V] pushed "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"["</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">spattern</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp">           <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp">   <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp">   <span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">setChromosomeVector</span><span class="p">(</span><span class="n" style="color: #333;">V</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">   <span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">printText</span><span class="p">(</span><span class="n" style="color: #333;">vout</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(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="LC72" class="line" lang="cpp">           <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TabEntry</span><span class="o" style="font-weight: 600;"><></span> <span class="k" style="font-weight: 600;">const</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 new_line" data-linenumber="73" style="width: 35px; color: rgba(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="LC73" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(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="LC74" class="line" lang="cpp">   <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">P</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(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="LC75" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(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="LC76" class="line" lang="cpp">   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(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="LC77" class="line" lang="cpp">           <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">,</span></span>

</pre>

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78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp">           <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">trie</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LinearHashTrie</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">shared_ptr_type</span></span>

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp">   <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Pcontig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">getContigNamesAndTrie</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp">   <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">line</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="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">readEntry</span><span class="p">()).</span><span class="n" style="color: #333;">first</span> <span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">   <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">)</span></span>

</pre>

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85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp">           <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp">                   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</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="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Pchr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">                   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">Pcontig</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">searchCompleteNoFailure</span><span class="p">(</span><span class="n" style="color: #333;">Pchr</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">,</span><span class="n" style="color: #333;">Pchr</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(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="LC89" class="line" lang="cpp">                   <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp">                           <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">).</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(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="LC91" class="line" lang="cpp">                           <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</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="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">).</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(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="LC92" class="line" lang="cpp"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

93

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp">                           <span class="n" style="color: #333;">vout</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">a</span><span class="p">);</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

94

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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="LC94" class="line" lang="cpp">                           <span class="n" style="color: #333;">vout</span><span class="p">.</span><span class="n" style="color: #333;">put</span><span class="p">(</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">);</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

95

</td>

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

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

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

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

<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp">                           <span class="n" style="color: #333;">line</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="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">

</td>

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

97

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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="LC97" class="line" lang="cpp"></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

98

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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="LC98" class="line" lang="cpp">                           <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">%</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="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="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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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

99

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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="LC99" class="line" lang="cpp">                                   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[V] "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</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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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">                  <span class="p">}</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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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

101

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

<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">else</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp">                  <span class="p">{</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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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp">                          <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LibMausException</span> <span class="n" style="color: #333;">lme</span><span class="p">;</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

104

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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="LC104" class="line" lang="cpp">                          <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">getStream</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[E] sequence "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">Pchr</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">,</span><span class="n" style="color: #333;">Pchr</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" does not appear in FastA file provided"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

105

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

<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp">                          <span class="n" style="color: #333;">lme</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

106

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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="LC106" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">lme</span><span class="p">;</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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

<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp">                  <span class="p">}</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

108

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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="LC108" class="line" lang="cpp">          <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="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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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

109

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

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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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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

110

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// vcf.unparsedCopy(vout);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">  <span class="c" style="color: #998; font-style: italic;">#if 0</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">       if ( Vin.size() )</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(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="LC115" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">       {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">               std::pair<bool, char const *> E;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">               {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                       libmaus2::aio::InputStreamInstance ISI(Vin[0]);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                       libmaus2::vcf::VCFParser vcf(ISI);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                       vcf.printText(vout);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                       vcf.unparsedCopy(vout);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">               }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">               for ( uint64_t j = 1; j < Vin.size(); ++j )</span></span>

</pre>

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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="cpp"><span class="c" style="color: #998; font-style: italic;">               {</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(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="LC127" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                       libmaus2::aio::InputStreamInstance ISI(Vin[j]);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                       libmaus2::vcf::VCFParser vcf(ISI);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(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="LC129" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                       vcf.unparsedCopy(vout);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">               }</span></span>

</pre>

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<td class="diff-line-num new new_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">

131

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">       }</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

132

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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="LC132" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">       #endif</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

133

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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="LC133" class="line" lang="cpp"></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

134

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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="LC134" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">gz</span> <span class="p">)</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

135

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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="LC135" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

136

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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="LC136" class="line" lang="cpp">          <span class="n" style="color: #333;">pBOS</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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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="LC137" class="line" lang="cpp">          <span class="n" style="color: #333;">pBOS</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">addEOFBlock</span><span class="p">();</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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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="LC138" class="line" lang="cpp">          <span class="n" style="color: #333;">pBOS</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>

</pre>

</td>

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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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<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">

139

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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="LC139" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

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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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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

140

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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="LC140" class="line" lang="cpp"></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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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="LC141" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</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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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

142

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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="LC142" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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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="LC143" class="line" lang="cpp"></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span></span>

</pre>

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<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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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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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="LC145" class="line" lang="cpp"><span class="p">{</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

146

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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="LC146" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">try</span></span>

</pre>

</td>

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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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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

147

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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="LC147" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

</td>

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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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<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">

148

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp">          <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgInfo</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">arginfo</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">);</span></span>

</pre>

</td>

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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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<td class="diff-line-num new new_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">

149

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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="LC149" class="line" lang="cpp"></span>

</pre>

</td>

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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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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

150

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</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;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

152

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp">                          <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</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="s" style="color: #d14;">"-v"</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

153

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp">                          <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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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">

154

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp">                          <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</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="s" style="color: #d14;">"--version"</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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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

155

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp">                  <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

156

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp">                  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_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">

157

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp">                          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">license</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

158

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

159

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp">                  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

160

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

161

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp">                          <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</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="s" style="color: #d14;">"-h"</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

162

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp">                          <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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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">

163

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp">                          <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</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="s" style="color: #d14;">"--help"</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp">                  <span class="p">)</span></span>

</pre>

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

165

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp">                  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(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="LC166" class="line" lang="cpp">                          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">license</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(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="LC167" class="line" lang="cpp">                          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

168

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp">                          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Key=Value pairs:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</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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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

169

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp">                          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

170

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"></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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<td class="diff-line-num new new_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">

171

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp">                          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></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="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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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

172

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"></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">

</td>

<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

173

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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="LC173" class="line" lang="cpp">                          <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span> <span class="s" style="color: #d14;">"verbose=<["</span><span class="o" style="font-weight: 600;">+::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">formatNumber</span><span class="p">(</span><span class="n" style="color: #333;">getDefaultVerbose</span><span class="p">())</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"]>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"print progress report (default: 1)"</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

174

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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="LC174" class="line" lang="cpp"></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

175

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp">                          <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">printMap</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</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="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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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

176

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"></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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<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">

177

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp">                          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

178

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</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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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

179

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp">                  <span class="p">}</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

180

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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="LC180" class="line" lang="cpp"></span>

</pre>

</td>

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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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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

181

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vcfreplacecontigs</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cin</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">);</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

182

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

183

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ex</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp">  <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

185

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp">          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ex</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

186

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>

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187

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"><span class="p">}</span></span></pre>

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