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GitLab

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<h3>

Étienne Mollier pushed to branch master

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/b36bccd15b79ea86c241f0014673225bb1d34854">b36bccd1</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-12T16:17:53+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.177+ds</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/1cba847418cae662bbf3130eee1d3839ff714a2b">1cba8474</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-12T16:17:53+01:00</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/f1564365466440630b83c4149f694674d723ec44">f1564365</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-12T16:17:54+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.0.177+ds'

Update to upstream version '2.0.177+ds'

with Debian dir 7084c20732c1d252c294ebab01aa0cbf12ecbb5a</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/8ca7a62521a69f5ea392e092ddd082ceccbb13a5">8ca7a625</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-18T11:19:27+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add myself to Uploaders

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/493b0ee73c5de468418f2a14e15c8bc098417015">493b0ee7</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-18T11:24:04+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">build depends on libmaus2-dev >= 2.0.749

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b22260ca4ff12bdf0c49fa0577be14f0d64d87bc">b22260ca</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-18T14:06:05+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add patches to fix various issues

manuals.patch targets manual pages issues reported by lintian.

spelling-error-in-binary.patch fixes one of the spelling issues

reported by lintian.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/009dc429aeb3bd3cd2f0489116071339fca263b5">009dc429</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-18T15:39:35+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">one last typo fix

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/bfc5cd7ddba5296ecd53e854866fa356808e0a22">bfc5cd7d</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-18T21:59:20+01:00</i>

</div>

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

</pre>

</li>

</ul>

<h4>20 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="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#41ef1acba73f4e416ef261e265eaaa2383872feb">

<span class="new-file">

+

debian/patches/manuals.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<span class="new-file">

+

debian/patches/series

</span>

</a>

</li>

<li class="file-stats">

<a href="#112a0772ac215bf87f8257be66adb66e6c8389b0">

<span class="new-file">

+

debian/patches/spelling-error-in-binary.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#dee5c4430f3aa3a43132ee80817c8d207bada8d9">

release.sh

</a>

</li>

<li class="file-stats">

<a href="#0cf1a4ac4c7f40ab2de2b4d5c207bafc2ad847a6">

<span class="new-file">

+

removespace.sh

</span>

</a>

</li>

<li class="file-stats">

<a href="#67e794015a01b8816bd16290e5f8538236da8245">

src/Makefile.am

</a>

</li>

<li class="file-stats">

<a href="#40ae775c772d41bff8f58cc32f7693b77a9497ac">

src/biobambam2/BamBamConfig.hpp.in

</a>

</li>

<li class="file-stats">

<a href="#9c542eb79cd228f3e3385d418f89d6b514f558e0">

src/biobambam2/UpdateNumericalIndex.cpp

</a>

</li>

<li class="file-stats">

<a href="#5393ade310e7cd11929979d7b18ab8cc6860e027">

src/programs/bamcollate2.cpp

</a>

</li>

<li class="file-stats">

<a href="#731c8a82cbe64a38ffc549ef39ae18a3c5470e9a">

src/programs/bamconsensus.cpp

</a>

</li>

<li class="file-stats">

<a href="#b8a20a8a09b5dbd365fb76fb83e47d3490234a84">

<span class="new-file">

+

src/programs/bamdifference.cpp

</span>

</a>

</li>

<li class="file-stats">

<a href="#f003bbc90ca3edf349c1e28704952dda9ef29682">

src/programs/bammerge.cpp

</a>

</li>

<li class="file-stats">

<a href="#be752f41aab032268ccb172abc929cf063a40400">

src/programs/bamtofastq.cpp

</a>

</li>

<li class="file-stats">

<a href="#5996963c0b0cac34c60d4ecc66918c31b32d6518">

src/programs/blastnxmltobam.cpp

</a>

</li>

<li class="file-stats">

<a href="#ab5115e6c5d8836f3f68486cbaf80c86d2df924f">

<span class="new-file">

+

src/programs/fastaselectreg.cpp

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="a5cc2925ca8258af241be7e5b0381edf30266302">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#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">

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,3 +70,5 @@ src/vcffiltersamples</td>

</tr>

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

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

70

</td>

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

70

</td>

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

<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">src/vcfdiff</span>

</pre>

</td>

</tr>

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

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

71

</td>

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

71

</td>

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

<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">src/vcffilterfilterflags</span>

</pre>

</td>

</tr>

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

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

72

</td>

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

72

</td>

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

<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext">src/vcfreplacecontigsmap</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<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">

73

</td>

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

<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">src/fastaselectreg</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<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">

74

</td>

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

<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">src/bamdifference</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>

<hr>

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

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

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

</td>

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

1

</td>

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">biobambam2 (2.0.177-1) unstable; urgency=medium</span>

</pre>

</td>

</tr>

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

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

</td>

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

2

</td>

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

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

</pre>

</td>

</tr>

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

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

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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

</td>

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

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

</pre>

</td>

</tr>

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

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

</td>

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

4

</td>

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

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

</pre>

</td>

</tr>

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

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

</td>

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

5

</td>

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 12 Nov 2020 10:39:59 +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="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

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

</td>

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

7

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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 (2.0.176-1) 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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

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

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

</pre>

</td>

</tr>

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

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

</td>

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

9

</td>

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  * Adapt UpdateNumericalIndex to new libmaus2 api</span>

</pre>

</td>

</tr>

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

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

</td>

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

10

</td>

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">  * Fix output of orphaned read 2 instances in bamtofastq when splitting by readgroup</span>

</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">  * Remove references to non functional IRODS interface in libmaus2</span>

</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">  * Add bamdifference 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="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"></span>

</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"> -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 12 Nov 2020 09:43:13 +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="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"></span>

</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">biobambam2 (2.0.175-1) 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="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"></span>

</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">  * Add fastaselectreg</span>

</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"></span>

</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"> -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 27 Aug 2020 10:08:12 +0200</span>

</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"></span>

</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">biobambam2 (2.0.174-1) 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="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">  * Fix wrong operator for deallocating memory in bamconsensus</span>

</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"> -- German Tischler-Höhle <germant@miltenyibiotec.de>  Mon, 10 Aug 2020 11:26:08 +0200</span>

</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" id="" style="line-height: 1.6;">

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

1

</td>

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28

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">biobambam2 (2.0.173-1) unstable; urgency=medium</span>

</pre>

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2

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29

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

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3

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30

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">  * Fix for libmaus2 update</span>

</pre>

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<br>

</li>

<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#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(biobambam2,2.0.17<span class="idiff left right">3</span>,[germant@miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])</span>

</pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT(biobambam2,2.0.17<span class="idiff left right">7</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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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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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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166

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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 >= 2.0.74<span class="idiff left right">0</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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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.74<span class="idiff left right">9</span>])</span>

</pre>

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

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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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<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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<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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<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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<pre style="margin: 0;"> <span id="LC302" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="plaintext">    PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.74<span class="idiff left right">0</span>])</span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">    PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.74<span class="idiff left right">9</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="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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<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 bamfilterbyname bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus vcfreplacecontigs vcffiltersamples bamexploderg bamexondepth bamheadercat bammarkduplicatesoptdist vcfdiff bamsimpledepth bamdepthmerge bamcountflags vcffilterfilterflags vcfreplacecontigsmap"</span>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext">UNCOMMON="bamfilter bamfilterbyname bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus vcfreplacecontigs vcffiltersamples bamexploderg bamexondepth bamheadercat bammarkduplicatesoptdist vcfdiff bamsimpledepth bamdepthmerge bamcountflags vcffilterfilterflags vcfreplacecontigsmap<span class="idiff left right"> fastaselectreg</span>"</span>

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

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="plaintext">UNCOMMONUNINSTALLED=</span>

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

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">biobambam2 (2.0.17<span class="idiff left right">3+ds-2) UNRELEASED</span>; urgency=medium</span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">biobambam2 (2.0.17<span class="idiff left right">7+ds-1) unstable</span>; urgency=medium</span>

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

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">  * <span class="idiff left right">Team upload</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * <span class="idiff left right">Add myself to Uploaders.</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  * Remove the zlib1g-dev dependency, as zlib1g should now be properly pulled</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">    and used by libmaus2 (>= 2.0.740+dfsg-2).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Force builds against libmaus2 >= 2.0.749.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Add manuals.patch to fix various issues reported by lintian.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">  * Add spelling-error-in-binary.patch.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org>  <span class="idiff left right">Mon, 10 Aug 2020 21:22:20 +02</span>00</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org>  <span class="idiff left right">Wed, 18 Nov 2020 21:58:28 +01</span>00</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">biobambam2 (2.0.173+ds-1) unstable; urgency=medium</span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: biobambam2</span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">           Étienne Mollier <etienne.mollier@mailoo.org></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               pkg-config,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">               libmaus2-dev (>= 2.0.74<span class="idiff left right">0+dfsg-2</span>)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">               libmaus2-dev (>= 2.0.74<span class="idiff left right">9</span>)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.0</span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/biobambam2</span>

</pre>

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11

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git</span>

</pre>

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<br>

</li>

<li id="41ef1acba73f4e416ef261e265eaaa2383872feb">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#41ef1acba73f4e416ef261e265eaaa2383872feb"><strong>debian/patches/manuals.patch</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: miscellaneous manual pages fixes</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-11-18</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">---</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bamalignfrac.1</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bamalignfrac.1</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> .TH BAMALIGNFRAC 1 "July 2019" BIOBAMBAM</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> .SH NAME</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bamalignfrac - compute fraction of aligned bases in alignment file</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bamalignfrac \- compute fraction of aligned bases in alignment file</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> .SH SYNOPSIS</span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> .PP</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> .B bamalignfrac</span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -10,30 +10,31 @@</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> bamalignfrac reads a SAM/BAM/CRAM file, computes a set of statistical values</span>

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<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

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> and outputs these on the standard output channel. The values produced are</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<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="diff"> </span>

</pre>

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<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

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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="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</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="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

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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="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the number of names passing a given regex filter</span></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</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="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

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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="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the number of names passing a given regex filter</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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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="LC25" class="line" lang="diff"> </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="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

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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="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</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="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

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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="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the number of primary alignments</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="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

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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="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</pre>

</td>

</tr>

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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="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

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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="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the number of primary alignments</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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<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="diff"> </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="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

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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="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</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="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">

32

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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="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the number of total alignments</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="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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

<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</pre>

</td>

</tr>

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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="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">

34

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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="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the number of total alignments</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="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

</td>

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

<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</pre>

</td>

</tr>

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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="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">

37

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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="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the total number of bases</span></span>

</pre>

</td>

</tr>

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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="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">

38

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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="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</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="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

39

</td>

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

<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the total number of bases</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="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="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">

40

</td>

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

<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>

</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">

</td>

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

41

</td>

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

<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</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">

</td>

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

42

</td>

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

<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the total number of aligned bases</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

43

</td>

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

<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

</td>

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

<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the total number of aligned bases</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

45

</td>

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

<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>

</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">

</td>

<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

</td>

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

<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</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">

</td>

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

47

</td>

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

<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the fraction of aligned bases</span></span>

</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">

</td>

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

48

</td>

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

<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</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">

</td>

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

49

</td>

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

<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the fraction of aligned bases</span></span>

</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">

</td>

<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

</td>

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

<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>

</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">

</td>

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

51

</td>

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

<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

52

</td>

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

<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the total number of clipped/unaligned bases</span></span>

</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">

</td>

<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">

53

</td>

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

<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</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">

</td>

<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">

54

</td>

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

<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the total number of clipped/unaligned bases</span></span>

</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">

</td>

<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">

55

</td>

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

<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>

</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">

</td>

<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">

56

</td>

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

<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</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">

</td>

<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">

57

</td>

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

<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the number of unmapped reads</span></span>

</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">

</td>

<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">

58

</td>

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

<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</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">

</td>

<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">

59

</td>

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

<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the number of unmapped reads</span></span>

</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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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>

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61

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PP</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> These values are printed on the standard output channel at the end of the</span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> program run in the last line printed by the program. The program prints a</span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> set of line description line prior to that.</span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -42,8 +43,12 @@</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> The input file needs to be provied in query name sorted order, which can be</span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> obtained via e.g.</span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bamsort SO=queryname</span></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PP</span></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.EX</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        $ bamsort SO=queryname</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.EE</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PP</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> right before being passed to bamalignfrac.</span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> The following key=value pairs can be given:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bamauxmerge.1</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bamauxmerge.1</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="p">@@ -8,34 +8,33 @@</span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> in_unmapped in_mapped</span>

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83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> .SH DESCRIPTION</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">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> bamauxmerge reads and merges two SAM/BAM/CRAM files which are expected to have the</span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-following properties</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+following properties:</span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the first file contains only unmapped reads and it's header contains no SQ lines</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the first file contains only unmapped reads and it's header contains no SQ lines</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the second file was produced by an aligner based on the content of the first file.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the order of the reads is the same in the first an second file</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</pre>

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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">

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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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the second file was produced by an aligner based on the content of the first file.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>

</pre>

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101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</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="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

</td>

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

<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the order of the reads is the same in the first an second file</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> into a single alignment file.</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="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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</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="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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PP</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="diff"> The headers of the two files are merged in the following file:</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="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="diff"> </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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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the SQ lines contained in the header of the second file are appended to the header of the first file to obtain the header of the output file</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

</td>

</tr>

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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="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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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="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It</span></span>

</pre>

</td>

</tr>

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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="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

112

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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="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* all other header information from the second file is discarded</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="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

113

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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="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

</td>

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

<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the SQ lines contained in the header of the second file are appended to the header of the first file to obtain the header of the output file</span></span>

</pre>

</td>

</tr>

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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="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">

115

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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="LC115" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

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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="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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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="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</pre>

</td>

</tr>

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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="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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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="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+all other header information from the second file is discarded</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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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="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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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="LC119" class="line" lang="diff"> The output records are constructed in the following way:</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="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

120

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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="LC120" class="line" lang="diff"> </span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

121

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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="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-1. Take a record from the second file</span></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP 1.</span></span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Take a record from the second file</span></span>

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

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-2. Copy all aux fields from the corresponding record in the first file which are not already present.</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP 2.</span></span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Copy all aux fields from the corresponding record in the first file which are not already present.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> The following key=value pairs can be given:</span>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bamauxmerge2.1</span></span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bamauxmerge2.1</span></span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="p">@@ -10,46 +10,44 @@</span></span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> bamauxmerge2 reads and merges two BAM files which are expected to have the</span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> following properties</span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the first file contains only unmapped reads and it's header contains no SQ lines</span></span>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the first file contains only unmapped reads and it's header contains no SQ lines</span></span>

</pre>

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<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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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> </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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</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="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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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the second file was produced by an aligner based on the content of the first file.</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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</pre>

</td>

</tr>

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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="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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the second file was produced by an aligner based on the content of the first file.</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> </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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* both files are sorted in query name order</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</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="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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-into a single alignment file.</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+both files are sorted in query name order into a single alignment file.</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> </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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PP</span></span>

</pre>

</td>

</tr>

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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="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="diff"> The headers of the two files are merged in the following file:</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="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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</span></span>

</pre>

</td>

</tr>

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

<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+the SQ lines contained in the header of the second file are appended to the header of the first file to obtain the header of the output file</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</pre>

</td>

</tr>

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

<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* the SQ lines contained in the header of the second file are appended to the header of the first file to obtain the header of the output file</span></span>

</pre>

</td>

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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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</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="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">

164

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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="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* all other header information from the second file is discarded</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="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">

166

</td>

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

<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

</td>

</tr>

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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="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">

167

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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="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP *</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+all other header information from the second file is discarded</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PP</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> The output records are constructed in the following way:</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> </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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</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="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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-1. Take a record from the second file</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="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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP 1.</span></span>

</pre>

</td>

</tr>

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

<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Take a record from the second file</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> </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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</pre>

</td>

</tr>

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

<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-2. Copy all aux fields from the corresponding record in the first file which are not already present.</span></span>

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

<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP 2.</span></span>

</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="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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Copy all aux fields from the corresponding record in the first file which are not already present.</span></span>

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

<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> </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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</pre>

</td>

</tr>

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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="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">

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-3. Reinsert clipped adapter bases/quality values stored in the qs/qq by</span></span>

</pre>

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184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP 3.</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Reinsert clipped adapter bases/quality values stored in the qs/qq by</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="diff"> aux fields by fastqtobam2 and remove the qs/qq aux fields while inserting</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

187

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> appropriate soft clipping CIGAR operations.</span>

</pre>

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188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-4. Fix mate information like bamfixmateinformation.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP 4.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Fix mate information like bamfixmateinformation.</span></span>

</pre>

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193

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-5. Insert the mate CIGAR information fields MC and MS if the mate is aligned.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP 5.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Insert the mate CIGAR information fields MC and MS if the mate is aligned.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.It Cm</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-6. Insert the MQ (mate quality) aux field.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.IP 6.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Insert the MQ (mate quality) aux field.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> The following key=value pairs can be given:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bamcollate2.1</span></span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bamcollate2.1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="p">@@ -196,7 +196,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> the input SAM/BAM/CRAM file is used (and filtered in case of reset=1).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> .B resetaux=<0|1>:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-remove auxilliary fields if resetaux=1. This key is only available for</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+remove auxiliary fields if resetaux=1. This key is only available for</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> reset=1. If reset=1 then the default is to remove all aux fields.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> .B auxfilter=<>:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bamconsensus.1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bamconsensus.1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="p">@@ -25,7 +25,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> .B E is the end position on the reference sequence (exclusive)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-The reference key specifiying the name of a FastA reference sequence file</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+The reference key specifying the name of a FastA reference sequence file</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> is required. The consensus is constructed by computing heavy paths in local</span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> DeBruijn graphs. Consequently it is usually a patchwork of the haplotypes</span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> present for diploid/polyploid genomes.</span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bammarkduplicates.1</span></span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bammarkduplicates.1</span></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="p">@@ -95,7 +95,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> .IP 0:</span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> duplicates will be retained in the output file and have the duplication flag set</span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> .IP 1:</span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-duplicates will be remove when writing the output file</span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+duplicates will be removed when writing the output file</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> .PP</span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> .B md5=<0|1>:</span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> md5 checksum creation for output file. Valid values are</span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="p">@@ -133,11 +133,11 @@</span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> this option works like the tag option but is restricted to sequences of</span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> nucleotides (A,C,G or T) as tags. The length of each tag sequence is not</span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> allowed to exceed 15 bases. All tags are required to have the same length.</span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Each non nucleotide symbol is mapped to A. In constrast to the tag option, </span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Each non nucleotide symbol is mapped to A. In contrast to the tag option,</span></span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> nucltag uses less memory for processing and can be expected to be faster.</span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> .PP</span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> .B D</span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ouptut file name for removed duplicates if rmdup=1. By default the reads and</span></span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+output file name for removed duplicates if rmdup=1. By default the reads and</span></span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> read pairs marked as duplicates are discarded when rmdup=1. If the D key is</span>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> set, then the sequence of reads which is not written to the output file is</span>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> written to a separate file. The name of this separate file is the value of</span>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bammarkduplicates2.1</span></span>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bammarkduplicates2.1</span></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="p">@@ -96,7 +96,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> .IP 0:</span>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> duplicates will be retained in the output file and have the duplication flag set</span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> .IP 1:</span>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-duplicates will be remove when writing the output file</span></span>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+duplicates will be removed when writing the output file</span></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> .PP</span>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> .B maxreadlength=<[500]>:</span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> maximum read length in input. This value can be set higher than the actual</span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="p">@@ -138,11 +138,11 @@</span></span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> this option works like the tag option but is restricted to sequences of</span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> nucleotides (A,C,G or T) as tags. The length of each tag sequence is not</span>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> allowed to exceed 15 bases. All tags are required to have the same length.</span>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Each non nucleotide symbol is mapped to A. In constrast to the tag option, </span></span>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Each non nucleotide symbol is mapped to A. In contrast to the tag option,</span></span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> nucltag uses less memory for processing and can be expected to be faster.</span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> .PP</span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> .B D</span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ouptut file name for removed duplicates if rmdup=1. By default the reads and</span></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+output file name for removed duplicates if rmdup=1. By default the reads and</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> read pairs marked as duplicates are discarded when rmdup=1. If the D key is</span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> set, then the sequence of reads which is not written to the output file is</span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> written to a separate file. The name of this separate file is the value of</span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bammarkduplicatesopt.1</span></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bammarkduplicatesopt.1</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="p">@@ -98,7 +98,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> .IP 0:</span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> duplicates will be retained in the output file and have the duplication flag set</span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> .IP 1:</span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-duplicates will be remove when writing the output file</span></span>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+duplicates will be removed when writing the output file</span></span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> .PP</span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> .B md5=<0|1>:</span>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> md5 checksum creation for output file. Valid values are</span>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="p">@@ -136,11 +136,11 @@</span></span>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> this option works like the tag option but is restricted to sequences of</span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> nucleotides (A,C,G or T) as tags. The length of each tag sequence is not</span>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> allowed to exceed 15 bases. All tags are required to have the same length.</span>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Each non nucleotide symbol is mapped to A. In constrast to the tag option, </span></span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Each non nucleotide symbol is mapped to A. In contrast to the tag option,</span></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> nucltag uses less memory for processing and can be expected to be faster.</span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> .PP</span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> .B D</span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ouptut file name for removed duplicates if rmdup=1. By default the reads and</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+output file name for removed duplicates if rmdup=1. By default the reads and</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> read pairs marked as duplicates are discarded when rmdup=1. If the D key is</span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> set, then the sequence of reads which is not written to the output file is</span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> written to a separate file. The name of this separate file is the value of</span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bammaskflags.1</span></span>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bammaskflags.1</span></span>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> .TH BAMMASKFLAGS 1 "July 2013" BIOBAMBAM</span>

</pre>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> .SH NAME</span>

</pre>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bammaskflags - remove flags from alignments</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bammaskflags \- remove flags from alignments</span></span>

</pre>

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310

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> .SH SYNOPSIS</span>

</pre>

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311

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> .PP</span>

</pre>

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312

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> .B bammaskflags</span>

</pre>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="p">@@ -24,7 +24,9 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> zlib/gzip level 9 (best) compression</span>

</pre>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> .P</span>

</pre>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> If libmaus has been compiled with support for igzip (see</span>

</pre>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.UR https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Intel article on igzip</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.UE )</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> then an additional valid value is</span>

</pre>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> .IP 11:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> igzip compression</span>

</pre>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="p">@@ -34,30 +36,42 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> complement of this number and the flag field of the reads/alignments in the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> input BAM file). This value can be obtained by adding up the following</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="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

327

</td>

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

<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> values of the flags:</span>

</pre>

</td>

</tr>

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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="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

328

</td>

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

<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP PAIRED (paired in sequencing):</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

329

</td>

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

<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

330

</td>

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

<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> 1</span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

331

</td>

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

<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP PROPER_PAIR (mapped as a proper pair):</span></span>

</pre>

</td>

</tr>

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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="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

332

</td>

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

<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PAIRED (paired in sequencing)</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

333

</td>

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

<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

334

</td>

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

<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> 2</span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

335

</td>

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

<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP UNMAP (unmapped):</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

336

</td>

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

<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PROPER_PAIR (mapped as a proper pair)</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

337

</td>

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

<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

338

</td>

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

<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> 4</span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

339

</td>

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

<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP MUNMAP (mate unmapped):</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

340

</td>

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

<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+UNMAP (unmapped)</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

341

</td>

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

<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

342

</td>

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

<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> 8</span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

343

</td>

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

<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP REVERSE (mapped to the reverse strand):</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

344

</td>

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

<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MUNMAP (mate unmapped)</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

345

</td>

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

<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

346

</td>

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

<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> 16</span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

347

</td>

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

<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP MREVERSE (mate mapped to the reverse strand):</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

348

</td>

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

<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+REVERSE (mapped to the reverse strand)</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

349

</td>

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

<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

350

</td>

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

<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> 32</span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

351

</td>

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

<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP READ1 (first read of pair):</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

352

</td>

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

<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MREVERSE (mate mapped to the reverse strand)</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

353

</td>

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

<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

354

</td>

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

<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> 64</span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

355

</td>

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

<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP READ2 (second read of pair):</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

356

</td>

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

<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+READ1 (first read of pair)</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

357

</td>

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

<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

358

</td>

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

<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> 128</span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

359

</td>

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

<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP SECONDARY (secondary alignment):</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

360

</td>

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

<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+READ2 (second read of pair)</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

361

</td>

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

<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

362

</td>

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

<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> 256</span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

363

</td>

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

<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP QCFAIL (failed quality control):</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

364

</td>

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

<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SECONDARY (secondary alignment)</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

365

</td>

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

<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

366

</td>

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

<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> 512</span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

367

</td>

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

<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP DUP (duplicate):</span></span>

</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

368

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+QCFAIL (failed quality control)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

369

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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="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

370

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> 1024</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="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

371

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.IP SUPPLEMENTARY (supplementary):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

372

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

<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DUP (duplicate)</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="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

373

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

<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

374

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

<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> 2048</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

375

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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="LC375" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SUPPLEMENTARY (supplementary)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

376

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

<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> .PP</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="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

377

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> .B tmpfile=<filename>: </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

378

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> prefix for temporary files. By default the temporary files are created in the current directory</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

379

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bammdnm.1</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

380

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bammdnm.1</span></span>

</pre>

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381

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span></span>

</pre>

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382

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> [options]</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

383

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"> .SH DESCRIPTION</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

384

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

<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> bammdnm reads a coordinate sorted BAM file from standard input, fills the</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

385

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-MD and NM auxilliary fields for each mapped read fragment and writes</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

386

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

<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MD and NM auxiliary fields for each mapped read fragment and writes</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

387

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> the resulting data to a BAM file on standard output.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

388

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> The following key=value pairs can be given:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bamreset.1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bamreset.1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="p">@@ -109,7 +109,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> read is marked as supplementary alignment</span>

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> .B resetaux=<0|1>:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-auxilliary fields (default).</span></span>

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+auxiliary fields (default).</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"> .B resetsortorder=<0|1>:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> set sort order to unknown if resetsortorder=1 (default) and leave as it is</span>

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bamsort.1</span></span>

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bamsort.1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="p">@@ -220,7 +220,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> this option works like the tag option but is restricted to sequences of</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC405" class="line" lang="diff"> nucleotides (A,C,G or T) as tags. The length of each tag sequence is not</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> allowed to exceed 15 bases. All tags are required to have the same length.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Each non nucleotide symbol is mapped to A. In constrast to the tag option, </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Each non nucleotide symbol is mapped to A. In contrast to the tag option,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> nucltag uses less memory for processing and can be expected to be faster.</span>

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> .PP</span>

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> .B M=<stderr>: </span>

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bamstreamingmarkduplicates.1</span></span>

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bamstreamingmarkduplicates.1</span></span>

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> adddupmarksupport=1, marks duplicate read pairs and reads and writes the</span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> resulting file in BAM, SAM or CRAM format. The preprocessing of the file</span>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> using bamsort with the stated options is mandatory, i.e.</span>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bamstreamingmarkduplicates will fail without it. In constrast to</span></span>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bamstreamingmarkduplicates will fail without it. In contrast to</span></span>

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> bammarkduplicates and bammarkduplicates2 the streaming variant</span>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> bamstreamingmarkduplicates processes the file in a single pass.</span>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> bamstreamingmarkduplicates cannot handle files containing orphan pair ends</span>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="p">@@ -129,7 +129,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> this option works like the tag option but is restricted to sequences of</span>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> nucleotides (A,C,G or T) as tags. The length of each tag sequence is not</span>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> allowed to exceed 15 bases. All tags are required to have the same length.</span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Each non nucleotide symbol is mapped to A. In constrast to the tag option, </span></span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Each non nucleotide symbol is mapped to A. In contrast to the tag option,</span></span>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> nucltag uses less memory for processing and can be expected to be faster.</span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> .B filterdupmarktags=<[0]>:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/fastqtobam.1</span></span>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/fastqtobam.1</span></span>

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="p">@@ -63,7 +63,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"> additional BAM encoding helper threads.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> .PP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> .B PGID=<></span>

</pre>

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-read group identifier for reads. By default no read group identifer is set.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+read group identifier for reads. By default no read group identifier is set.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> The fields CN, DS, DT, FO, KS, LB, PG, PI, PL, PU and SM of the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> corresponding @RG header line can be set by using the keys RGCN, RGDS, etc.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> respectively.</span></pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">manuals.patch</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">spelling-error-in-binary.patch</span></pre>

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<br>

</li>

<li id="112a0772ac215bf87f8257be66adb66e6c8389b0">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#112a0772ac215bf87f8257be66adb66e6c8389b0"><strong>debian/patches/spelling-error-in-binary.patch</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix spelling-error-in-binary</span></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-11-18</span></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">---</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- biobambam2.orig/src/programs/bamvalidate.cpp</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ biobambam2/src/programs/bamvalidate.cpp</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -282,8 +282,8 @@</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">                          std::vector< std::pair<std::string,std::string> > V;</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         V.push_back ( std::pair<std::string,std::string> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print stats at the end of a successfull run" ) );</span></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         V.push_back ( std::pair<std::string,std::string> ( "basequalhist=<["+::biobambam2::Licensing::formatNumber(getDefaultBaseQualHist())+"]>", "print base quality histogram at end of a successfull run" ) );</span></span>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                         V.push_back ( std::pair<std::string,std::string> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print stats at the end of a successful run" ) );</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                         V.push_back ( std::pair<std::string,std::string> ( "basequalhist=<["+::biobambam2::Licensing::formatNumber(getDefaultBaseQualHist())+"]>", "print base quality histogram at end of a successful run" ) );</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff">                          V.push_back ( std::pair<std::string,std::string> ( "passthrough=<["+::biobambam2::Licensing::formatNumber(getDefaultPassThrough())+"]>", "write alignments to standard output (default: do not pass through)" ) );</span>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff">                          V.push_back ( std::pair<std::string,std::string> ( "tmpfile=<filename>", "prefix for temporary files, default: create files in current directory (passthrough=1, index=1 only)" ) );</span>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff">                          V.push_back ( std::pair<std::string,std::string> ( "md5=<["+::biobambam2::Licensing::formatNumber(getDefaultMD5())+"]>", "create md5 check sum (default: 0, passthrough=1 only)" ) );</span></pre>

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<br>

</li>

<li id="dee5c4430f3aa3a43132ee80817c8d207bada8d9">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#dee5c4430f3aa3a43132ee80817c8d207bada8d9"><strong>release.sh</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/bash</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-euxo</span> pipefail</span>

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

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># update branches</span></span>

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4

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell">git checkout experimental</span>

</pre>

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<br>

</li>

<li id="0cf1a4ac4c7f40ab2de2b4d5c207bafc2ad847a6">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#0cf1a4ac4c7f40ab2de2b4d5c207bafc2ad847a6"><strong>removespace.sh</strong></a>

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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="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/bash</span></span>

</pre>

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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="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find src <span class="nt" style="color: #000080;">-regex</span> .<span class="k" style="font-weight: 600;">*</span><span class="se" style="color: #d14;">\\\.</span><span class="o" style="font-weight: 600;">[</span>ch]pp<span class="sb" style="color: #d14;">`</span> <span class="sb" style="color: #d14;">`</span>find src <span class="nt" style="color: #000080;">-regex</span> .<span class="k" style="font-weight: 600;">*</span><span class="se" style="color: #d14;">\\\.</span><span class="o" style="font-weight: 600;">[</span>ch]<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</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="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="shell"><span class="k" style="font-weight: 600;">      </span><span class="nv" style="color: #008080;">ORIG</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$i</span><span class="sb" style="color: #d14;">`</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="shell">  <span class="nv" style="color: #008080;">PATCHED</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>perl <span class="nt" style="color: #000080;">-p</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"s/(</span><span class="se" style="color: #d14;">\s</span><span class="s2" style="color: #d14;">*)(</span><span class="nv" style="color: #008080;">$)</span><span class="s2" style="color: #d14;">/</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">/"</span> < <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">i</span><span class="k" style="font-weight: 600;">}</span><span class="sb" style="color: #d14;">`</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="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="shell">  </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="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell">  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ORIG</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$PATCHED</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</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="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="shell"><span class="k" style="font-weight: 600;">              </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PATCHED</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">i</span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

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

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell">          <span class="c" style="color: #998; font-style: italic;"># git add ${i}</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">          <span class="nb" style="color: #0086b3;">echo</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">i</span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

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

10

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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="shell"> <span class="k" style="font-weight: 600;">fi</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="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

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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="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>

</td>

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<br>

</li>

<li id="67e794015a01b8816bd16290e5f8538236da8245">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#67e794015a01b8816bd16290e5f8538236da8245"><strong>src/Makefile.am</strong></a>

<hr>

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

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -152,7 +152,8 @@ EXTRA_PROGRAMS = blastnxmltobam \</td>

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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

152

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<td class="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

152

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="make"> vcfdiff <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

153

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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

153

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

<pre style="margin: 0;"> <span id="LC153" class="line" lang="make"> bamsimpledepth <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

154

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<td class="diff-line-num new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

154

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="make"> bamdepthmerge <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

155

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<td class="diff-line-num new_line old" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC155" class="line" lang="make"> bamcountflags</span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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="make"> bamcountflags <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

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

<pre style="margin: 0;">+<span id="LC156" class="line" lang="make"> fastaselectreg</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

156

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<td class="diff-line-num new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

157

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

<pre style="margin: 0;"> <span id="LC157" class="line" lang="make"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

157

</td>

<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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

<pre style="margin: 0;"> <span id="LC158" 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>

</td>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

</td>

<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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

<pre style="margin: 0;"> <span id="LC159" class="line" lang="make"><span class="nv" style="color: #008080;">populaterefcache_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${LIBMAUS2LIBS}</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="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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -703,3 +704,8 @@ bamcountflags_SOURCES = programs/bamcountflags.cpp biobambam2/Licensing.cpp</td>

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

<pre style="margin: 0;"> <span id="LC704" class="line" lang="make"><span class="nv" style="color: #008080;">bamcountflags_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${LIBMAUS2LIBS}</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="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

</td>

<td class="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC705" class="line" lang="make"><span class="nv" style="color: #008080;">bamcountflags_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>

</td>

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<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="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

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

<pre style="margin: 0;"> <span id="LC706" class="line" lang="make"><span class="nv" style="color: #008080;">bamcountflags_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>

</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="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

707

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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="LC707" class="line" lang="make"></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="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_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">

708

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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="LC708" class="line" lang="make"><span class="nv" style="color: #008080;">fastaselectreg_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> programs/fastaselectreg.cpp biobambam2/Licensing.cpp</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="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

709

</td>

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

<pre style="margin: 0;">+<span id="LC709" class="line" lang="make"><span class="nv" style="color: #008080;">fastaselectreg_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${LIBMAUS2LIBS}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

710

</td>

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

<pre style="margin: 0;">+<span id="LC710" class="line" lang="make"><span class="nv" style="color: #008080;">fastaselectreg_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>

</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="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

711

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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="LC711" class="line" lang="make"><span class="nv" style="color: #008080;">fastaselectreg_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>

</td>

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</table>

<br>

</li>

<li id="40ae775c772d41bff8f58cc32f7693b77a9497ac">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#40ae775c772d41bff8f58cc32f7693b77a9497ac"><strong>src/biobambam2/BamBamConfig.hpp.in</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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,6 @@</td>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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

<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">@LIBMAUS2IOLIBDEFINE@</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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

<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">@BIOBAMBAM_HAVE_XERCES_C@</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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

<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">@BIOBAMBAM_HAVE_GMP@</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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">@LIBMAUS2IRODSDEFINE@</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

</td>

<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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

<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">@HAVE_PTHREAD_MUTEX_RECURSIVE_NP@</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">@HAVE_PTHREAD_MUTEX_RECURSIVE@</span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>

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<br>

</li>

<li id="9c542eb79cd228f3e3385d418f89d6b514f558e0">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#9c542eb79cd228f3e3385d418f89d6b514f558e0"><strong>src/biobambam2/UpdateNumericalIndex.cpp</strong></a>

<hr>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,13 @@ namespace biobambam2</td>

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">if</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;">GetFileSize</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fileExists</span><span class="p">(</span><span class="n" style="color: #333;">indexfn</span><span class="p">)</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp">           <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC31" 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;">replfn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexfn</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".repl"</span><span class="p">;</span></span>

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

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<pre style="margin: 0;">+<span id="LC32" 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;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OutputStreamInstance</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;">prepl</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">                           <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;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OutputStreamInstance</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp">                                   <span class="n" style="color: #333;">replfn</span></span>

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

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp">                   <span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp">                   <span class="c1" style="color: #998; font-style: italic;">// get index stats</span></span>

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

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp">                   <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">alcnt</span><span class="p">,</span> <span class="n" style="color: #333;">mod</span><span class="p">,</span> <span class="n" style="color: #333;">numblocks</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC40" 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="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,20 +66,33 @@ namespace biobambam2</td>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp">                                   <span class="c1" style="color: #998; font-style: italic;">// std::cerr << "replacing index position for " << i << " by " << start.first << "," << start.second << std::endl;</span></span>

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68

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" 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;">BamNumericalIndexGenerator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReplaceObject</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp">                                           <span class="n" style="color: #333;">blockid</span><span class="p">,</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">,</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">second</span></span>

</pre>

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71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">                                   <span class="p">).</span><span class="n" style="color: #333;">serialise</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prepl</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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="c" style="color: #998; font-style: italic;">#if 0</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                                        libmaus2::bambam::BamNumericalIndexGenerator::replaceValue(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                                                indexfn,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                                                blockid,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                                                start.first,</span></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">

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                                                start.second</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC79" 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="LC80" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">                                        #endif</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp">                                   <span class="n" style="color: #333;">highestSet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blockid</span><span class="p">;</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC83" class="line" lang="cpp">                           <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC84" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC85" class="line" lang="cpp">                   <span class="n" style="color: #333;">prepl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC86" class="line" lang="cpp">                   <span class="n" style="color: #333;">prepl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC87" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" 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;">BamNumericalIndexGenerator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">replaceValues</span><span class="p">(</span><span class="n" style="color: #333;">indexfn</span><span class="p">,</span><span class="n" style="color: #333;">replfn</span><span class="p">);</span></span>

</pre>

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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>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC90" 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;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FileRemoval</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">removeFile</span><span class="p">(</span><span class="n" style="color: #333;">replfn</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_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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<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>

</pre>

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

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp">                   <span class="c1" style="color: #998; font-style: italic;">// std::cerr << "shifting index positions for [" << highestSet+1 << "," << numblocks << ")" << " by " << static_cast<int64_t>(compdata.second.size()) - static_cast<int64_t>(compdata.first) << std::endl;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp">                   <span class="c1" style="color: #998; font-style: italic;">// shift values in part we moved as is</span></span>

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<pre style="margin: 0;">-<span id="LC75" 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;">BamNumericalIndexGenerator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shiftValues</span><span class="p">(</span></span>

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<td class="diff-line-num new old_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="LC95" 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;">BamNumericalIndexGenerator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shiftValues<span class="idiff left right">Streaming</span></span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp">                           <span class="n" style="color: #333;">indexfn</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp">                           <span class="n" style="color: #333;">highestSet</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;">numblocks</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp">                           <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">compdata</span><span class="p">.</span><span class="n" style="color: #333;">second</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="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">compdata</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span></span>

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<br>

</li>

<li id="5393ade310e7cd11929979d7b18ab8cc6860e027">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#5393ade310e7cd11929979d7b18ab8cc6860e027"><strong>src/programs/bamcollate2.cpp</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1403,29 +1403,14 @@ void bamcollate2(libmaus2::util::ArgInfo const & arginfo)</td>

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

</pre>

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<pre style="margin: 0;"> <span id="LC1404" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1405" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); 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="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1406" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); 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="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1407" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/irods/IRodsInputStreamFactory.hpp></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1408" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</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="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1409

</td>

<td class="diff-line-num new_line old" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1409" 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="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1410

</td>

<td class="diff-line-num new_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1406

</td>

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

<pre style="margin: 0;"> <span id="LC1406" 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>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1411

</td>

<td class="diff-line-num new_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1407

</td>

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

<pre style="margin: 0;"> <span id="LC1407" 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="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1412

</td>

<td class="diff-line-num new_line" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1408

</td>

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

<pre style="margin: 0;"> <span id="LC1408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1413

</td>

<td class="diff-line-num new_line" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1409

</td>

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

<pre style="margin: 0;"> <span id="LC1409" class="line" lang="cpp"> <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="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1414

</td>

<td class="diff-line-num new_line old" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1414" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</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="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1415

</td>

<td class="diff-line-num new_line old" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1415" 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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsInputStreamFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">registerHandler</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="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1416

</td>

<td class="diff-line-num new_line old" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1416" class="line" lang="cpp">                <span class="cp" style="color: #999; font-weight: 600;">#endif</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="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1417

</td>

<td class="diff-line-num new_line old" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1417" 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="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1418

</td>

<td class="diff-line-num new_line" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1410

</td>

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

<pre style="margin: 0;"> <span id="LC1410" 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;">timing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RealTimeClock</span> <span class="n" style="color: #333;">rtc</span><span class="p">;</span> <span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">start</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="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1419

</td>

<td class="diff-line-num new_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1411

</td>

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

<pre style="margin: 0;"> <span id="LC1411" 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="1420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1420

</td>

<td class="diff-line-num new_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1412

</td>

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

<pre style="margin: 0;"> <span id="LC1412" 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="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>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1421

</td>

<td class="diff-line-num new_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1413

</td>

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

<pre style="margin: 0;"> <span id="LC1413" class="line" lang="cpp"></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="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1422

</td>

<td class="diff-line-num new_line old" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1422" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</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="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1423

</td>

<td class="diff-line-num new_line old" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1423" class="line" lang="cpp">         <span class="c1" style="color: #998; font-style: italic;">// set program name for iRODS identification</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="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1424

</td>

<td class="diff-line-num new_line old" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1424" 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;">stringstream</span> <span class="n" style="color: #333;">irods_id</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="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1425

</td>

<td class="diff-line-num new_line old" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1425" class="line" lang="cpp">         <span class="n" style="color: #333;">irods_id</span>  <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PACKAGE_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;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getProgFileName</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">progname</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;">PACKAGE_VERSION</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="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1426

</td>

<td class="diff-line-num new_line old" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1426" class="line" lang="cpp">         <span class="n" style="color: #333;">setenv</span><span class="p">(</span><span class="n" style="color: #333;">SP_OPTION</span><span class="p">,</span> <span class="n" style="color: #333;">irods_id</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1427

</td>

<td class="diff-line-num new_line old" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1427" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1428

</td>

<td class="diff-line-num new_line old" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1428" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1429

</td>

<td class="diff-line-num new_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1414

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

<pre style="margin: 0;"> <span id="LC1414" 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 old_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1430

</td>

<td class="diff-line-num new_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1415

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<pre style="margin: 0;"> <span id="LC1415" 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 old_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1431

</td>

<td class="diff-line-num new_line" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1416

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

<pre style="margin: 0;"> <span id="LC1416" 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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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); 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="1511" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1526,14 +1511,6 @@ int main(int argc, char * argv[])</td>

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<td class="diff-line-num old_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1526

</td>

<td class="diff-line-num new_line" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1511

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<pre style="margin: 0;"> <span id="LC1511" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1527

</td>

<td class="diff-line-num new_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1512

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<pre style="margin: 0;"> <span id="LC1512" class="line" lang="cpp">         <span class="n" style="color: #333;">bamcollate2</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1528

</td>

<td class="diff-line-num new_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1513

</td>

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

<pre style="margin: 0;"> <span id="LC1513" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1529

</td>

<td class="diff-line-num new_line old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1529" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1530

</td>

<td class="diff-line-num new_line old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1530" class="line" lang="cpp">         <span class="c1" style="color: #998; font-style: italic;">// need a explicit call to disconnect to avoid atexit deallocation problems in iRODS 4.19+</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1531

</td>

<td class="diff-line-num new_line old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1531" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">defaultIrodsSystem</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1532

</td>

<td class="diff-line-num new_line old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1532" class="line" lang="cpp">         <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1533

</td>

<td class="diff-line-num new_line old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1533" class="line" lang="cpp">                         <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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getDefaultIRodsSystem</span><span class="p">())</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">disconnect</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1534

</td>

<td class="diff-line-num new_line old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1534" class="line" lang="cpp">         <span class="p">}</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1535

</td>

<td class="diff-line-num new_line old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1535" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1536

</td>

<td class="diff-line-num new_line old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1536" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1537

</td>

<td class="diff-line-num new_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1514

</td>

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<pre style="margin: 0;"> <span id="LC1514" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</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;">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;">"verbose"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultVerbose</span><span class="p">())</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC1515" 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;">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;">MemUsage</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" wall clock time "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">formatTime</span><span class="p">(</span><span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">getElapsedSeconds</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>

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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="cpp"> <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="731c8a82cbe64a38ffc549ef39ae18a3c5470e9a">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#731c8a82cbe64a38ffc549ef39ae18a3c5470e9a"><strong>src/programs/bamconsensus.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3307" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3307,7 +3307,7 @@ struct ReferenceCache</td>

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<pre style="margin: 0;"> <span id="LC3307" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC3308" 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="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">VuseCnt</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC3309" class="line" lang="cpp">         <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC3310" class="line" lang="cpp">                 <span class="n" style="color: #333;">Vref</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">RefEntry</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr_type</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC3310" class="line" lang="cpp">                 <span class="n" style="color: #333;">Vref</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RefEntry</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr_type</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC3311" 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] reference cache deallocating "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</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 old_line" data-linenumber="3312" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3312" class="line" lang="cpp">         <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC3313" class="line" lang="cpp"></span>

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<li id="b8a20a8a09b5dbd365fb76fb83e47d3490234a84">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#b8a20a8a09b5dbd365fb76fb83e47d3490234a84"><strong>src/programs/bamdifference.cpp</strong></a>

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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="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>

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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">

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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) 2009-2020 German Tischler-Höhle</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    Copyright (C) 2011-2013 Genome Research Limited</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC6" 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="LC7" 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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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC8" 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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<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">

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<pre style="margin: 0;">+<span id="LC9" 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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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"></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;">    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="LC12" 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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<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">

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<pre style="margin: 0;">+<span id="LC13" 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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<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">

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<pre style="margin: 0;">+<span id="LC14" 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="LC15" class="line" lang="cpp"></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;">    You should have received a copy of the GNU General Public License</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="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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<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">

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

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="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="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamBlockWriterBaseFactory.hpp></span></span>

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<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">

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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/bambam/BamWriter.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/bambam/BamHeaderUpdate.hpp></span></span>

</pre>

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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/util/ArgInfo.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 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="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamMultiAlignmentDecoderFactory.hpp></span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamPeeker.hpp></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/lz/BgzfDeflateOutputCallbackMD5.hpp></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BgzfDeflateOutputCallbackBamIndex.hpp></span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC30" 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;">getDefaultMD5</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>

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

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printVerbose</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;">errstr</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;">c0</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;">c1</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;">k</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;">verbose</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;">mod</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">c0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">c1</span><span class="p">)</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">mod</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">)</span></span>

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

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp">           <span class="n" style="color: #333;">errstr</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;">c0</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;">c1</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;">c0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">c1</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;">k</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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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp">   <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" 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 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 class="cm" style="color: #998; font-style: italic;"> * compute difference of two name sorted alignments files (SAM/BAM/CRAM)</span></span>

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

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<pre style="margin: 0;">+<span id="LC42" 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="LC43" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">bamintersect</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;">ArgParser</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arg</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC44" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC45" 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;">verbstr</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;">cerr</span><span class="p">;</span></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">

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<pre style="margin: 0;">+<span id="LC46" 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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mod</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"></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;">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;">ArgParser</span> <span class="n" style="color: #333;">arg0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">;</span></span>

</pre>

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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="n" style="color: #333;">arg0</span><span class="p">.</span><span class="n" style="color: #333;">replaceArg</span><span class="p">(</span><span class="s" style="color: #d14;">"I"</span><span class="p">,</span><span class="n" style="color: #333;">arg0</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="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="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;">ArgParser</span> <span class="n" style="color: #333;">arg1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">;</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp">   <span class="n" style="color: #333;">arg1</span><span class="p">.</span><span class="n" style="color: #333;">replaceArg</span><span class="p">(</span><span class="s" style="color: #d14;">"I"</span><span class="p">,</span><span class="n" style="color: #333;">arg0</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC52" class="line" lang="cpp"></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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"verbose"</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>

</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="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;">BamAlignmentDecoderWrapper</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;">decwrapper0</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;">BamMultiAlignmentDecoderFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">construct</span><span class="p">(</span><span class="n" style="color: #333;">arg0</span><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;">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;">BD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decwrapper0</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDecoder</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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamPeeker</span> <span class="n" style="color: #333;">BP0</span><span class="p">(</span><span class="n" style="color: #333;">BD0</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="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;">BamAlignment</span> <span class="n" style="color: #333;">algn0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" 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;">BamAlignmentDecoderWrapper</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;">decwrapper1</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;">BamMultiAlignmentDecoderFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">construct</span><span class="p">(</span><span class="n" style="color: #333;">arg1</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" 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;">BamAlignmentDecoder</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decwrapper1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDecoder</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;">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;">BamPeeker</span> <span class="n" style="color: #333;">BP1</span><span class="p">(</span><span class="n" style="color: #333;">BD1</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" 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;">BamAlignment</span> <span class="n" style="color: #333;">algn1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" 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;">md5filename</span><span class="p">;</span></span>

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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;">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="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;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfDeflateOutputCallback</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cbs</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC68" 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;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfDeflateOutputCallbackMD5</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;">Pmd5cb</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">getParsedArgOrDefault</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="p">(</span><span class="s" style="color: #d14;">"md5"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultMD5</span><span class="p">())</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp">   <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">if</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;">BamBlockWriterBaseFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getMD5FileName</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">()</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">                   <span class="n" style="color: #333;">md5filename</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;">getMD5FileName</span><span class="p">(</span><span class="n" style="color: #333;">arg</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="k" style="font-weight: 600;">else</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" 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] no filename for md5 given, not creating hash"</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="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">

75

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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">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">md5filename</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 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">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp">           <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfDeflateOutputCallbackMD5</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;">Tmd5cb</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</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;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfDeflateOutputCallbackMD5</span><span class="p">);</span></span>

</pre>

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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="n" style="color: #333;">Pmd5cb</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;">move</span><span class="p">(</span><span class="n" style="color: #333;">Tmd5cb</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 class="n" style="color: #333;">cbs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">Pmd5cb</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">());</span></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="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="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="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="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="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;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfDeflateOutputCallback</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Pcbs</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="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;">cbs</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 new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC85" class="line" lang="cpp">           <span class="n" style="color: #333;">Pcbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cbs</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp">   <span class="c1" style="color: #998; font-style: italic;">// construct writer</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC88" 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;">BamBlockWriterBase</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;">Pwriter</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;">BamBlockWriterBaseFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">construct</span><span class="p">(</span><span class="n" style="color: #333;">BD0</span><span class="p">.</span><span class="n" style="color: #333;">getHeader</span><span class="p">(),</span><span class="n" style="color: #333;">arg</span><span class="p">,</span><span class="n" style="color: #333;">Pcbs</span><span class="p">));</span></span>

</pre>

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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="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;">BamBlockWriterBase</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">wr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Pwriter</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">   <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">c0</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;">c1</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;">k</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="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">

92

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">BP1</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn1</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="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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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp">   <span class="p">{</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC95" 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;">name0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">algn0</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="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;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">algn1</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC97" 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;">r</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;">StrCmpNum</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">strcmpnum</span><span class="p">(</span><span class="n" style="color: #333;">name0</span><span class="p">,</span><span class="n" style="color: #333;">name1</span><span class="p">);</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp">           <span class="c1" style="color: #998; font-style: italic;">// name is in file0 but no in file1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">r</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="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">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">          <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" 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;">name0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">algn0</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">algn0</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name0</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp">                  <span class="p">{</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp">                          <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">getNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp">                          <span class="n" style="color: #333;">wr</span><span class="p">.</span><span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">);</span></span>

</pre>

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<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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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"></span>

</pre>

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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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c0</span><span class="p">;</span></span>

</pre>

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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 class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</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="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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<pre style="margin: 0;">+<span id="LC111" 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="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">                          <span class="n" style="color: #333;">printVerbose</span><span class="p">(</span><span class="n" style="color: #333;">verbstr</span><span class="p">,</span> <span class="n" style="color: #333;">c0</span><span class="p">,</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">mod</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">                  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp">          <span class="p">}</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="c1" style="color: #998; font-style: italic;">// name is in both files, drop data</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC116" 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 class="n" style="color: #333;">r</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="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp">          <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC118" 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;">algn0</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC119" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC120" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">algn0</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name</span> <span class="p">)</span></span>

</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="121" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC121" 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="122" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC122" class="line" lang="cpp">                          <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">getNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="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="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp">                          <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c0</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="125" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC125" class="line" lang="cpp">                          <span class="n" style="color: #333;">printVerbose</span><span class="p">(</span><span class="n" style="color: #333;">verbstr</span><span class="p">,</span> <span class="n" style="color: #333;">c0</span><span class="p">,</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">mod</span><span class="p">);</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">

126

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp">                  <span class="p">}</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">

127

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP1</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">algn1</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

128

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp">                  <span class="p">{</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">

129

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp">                          <span class="n" style="color: #333;">BP1</span><span class="p">.</span><span class="n" style="color: #333;">getNext</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"></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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c1</span><span class="p">;</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp">                          <span class="n" style="color: #333;">printVerbose</span><span class="p">(</span><span class="n" style="color: #333;">verbstr</span><span class="p">,</span> <span class="n" style="color: #333;">c0</span><span class="p">,</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">mod</span><span class="p">);</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp">                  <span class="p">}</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// name is only in file1, drop data</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC136" 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 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">

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp">          <span class="p">{</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC138" 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;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">algn1</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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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="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP1</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">algn1</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name1</span> <span class="p">)</span></span>

</pre>

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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 class="p">{</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp">                          <span class="n" style="color: #333;">BP1</span><span class="p">.</span><span class="n" style="color: #333;">getNext</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">);</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp">                          <span class="n" style="color: #333;">wr</span><span class="p">.</span><span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">);</span></span>

</pre>

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<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>

</pre>

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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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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp">                          <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c1</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="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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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp">                          <span class="n" style="color: #333;">printVerbose</span><span class="p">(</span><span class="n" style="color: #333;">verbstr</span><span class="p">,</span> <span class="n" style="color: #333;">c0</span><span class="p">,</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span><span class="n" style="color: #333;">mod</span><span class="p">);</span></span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC147" 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="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="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="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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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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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>

</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="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="c1" style="color: #998; font-style: italic;">// names only in file0 at end</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="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">getNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</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="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="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="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;">wr</span><span class="p">.</span><span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">);</span></span>

</pre>

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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>

</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="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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c0</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="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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</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="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>

</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="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">

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp">          <span class="n" style="color: #333;">printVerbose</span><span class="p">(</span><span class="n" style="color: #333;">verbstr</span><span class="p">,</span> <span class="n" style="color: #333;">c0</span><span class="p">,</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span><span class="n" style="color: #333;">mod</span><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="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">

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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="LC161" 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="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="n" style="color: #333;">Pwriter</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</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">

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"></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">

164

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">Pmd5cb</span> <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="n" style="color: #333;">Pmd5cb</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">saveDigestAsFile</span><span class="p">(</span><span class="n" style="color: #333;">md5filename</span><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">

166

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<pre style="margin: 0;">+<span id="LC166" 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="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">

167

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<pre style="margin: 0;">+<span id="LC167" 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="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="p">}</span></span>

</pre>

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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>

</pre>

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<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 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 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="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 class="k" style="font-weight: 600;">try</span></span>

</pre>

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<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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<pre style="margin: 0;">+<span id="LC173" 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="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">

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<pre style="margin: 0;">+<span id="LC174" 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;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Vformatcons</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="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">

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp">          <span class="n" style="color: #333;">Vformatcons</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;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="p">(</span><span class="s" style="color: #d14;">"h"</span><span class="p">,</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp">          <span class="n" style="color: #333;">Vformatcons</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;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="p">(</span><span class="s" style="color: #d14;">"v"</span><span class="p">,</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp">          <span class="n" style="color: #333;">Vformatcons</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;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</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="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>

</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">

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<pre style="margin: 0;">+<span id="LC179" 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;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Vformatin</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;">BamAlignmentDecoderInfo</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getArgumentDefinitions</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC180" 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;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Vformatout</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;">getArgumentDefinitions</span><span class="p">();</span></span>

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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>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC182" 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;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Vformat</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="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">

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<pre style="margin: 0;">+<span id="LC183" 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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mergeFormat</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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mergeFormat</span><span class="p">(</span><span class="n" style="color: #333;">Vformatin</span><span class="p">,</span><span class="n" style="color: #333;">Vformatout</span><span class="p">),</span><span class="n" style="color: #333;">Vformatcons</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC185" 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;">ArgParser</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">,</span><span class="n" style="color: #333;">Vformat</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"version"</span><span class="p">)</span> <span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC188" class="line" lang="cpp">          <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC189" 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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<pre style="margin: 0;">+<span id="LC190" 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>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC192" 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 class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</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="mi" style="color: #099;">2</span> <span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC193" class="line" lang="cpp">          <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC194" 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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<pre style="margin: 0;">+<span id="LC195" 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="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

196

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<pre style="margin: 0;">+<span id="LC196" 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;">"usage: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">arg</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;">" full.bam partial.bam"</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="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

197

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<pre style="margin: 0;">+<span id="LC197" 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="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

198

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<pre style="margin: 0;">+<span id="LC198" 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;">"Argument:"</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="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

199

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<pre style="margin: 0;">+<span id="LC199" 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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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

201

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<pre style="margin: 0;">+<span id="LC201" 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 new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

202

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

203

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<pre style="margin: 0;">+<span id="LC203" 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;">"-v/--verbose"</span><span class="p">,</span> <span class="s" style="color: #d14;">"print progress report"</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="204" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC204" 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;">"--md5 <["</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;">getDefaultMD5</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;">"create md5 check sum (default: 0)"</span> <span class="p">)</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="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="205" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC205" 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;">"--md5filename <filename>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"file name for md5 check sum (default: extend output file name)"</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="206" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC206" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" 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 new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC208" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC210" 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>

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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC211" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC212" 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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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bamintersect</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC217" 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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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp">  <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC219" 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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<pre style="margin: 0;">+<span id="LC220" 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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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="f003bbc90ca3edf349c1e28704952dda9ef29682">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#f003bbc90ca3edf349c1e28704952dda9ef29682"><strong>src/programs/bammerge.cpp</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="38" style="width: 35px; color: rgba(0,0,0,0.3); 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="38" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -38,10 +38,6 @@ static std::string getDefaultSortOrder() { return "coordinate"; }</td>

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<pre style="margin: 0;"> <span id="LC38" 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;">getDefaultMD5</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>

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39

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39

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<pre style="margin: 0;"> <span id="LC39" 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;">getDefaultIndex</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 old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/irods/IRodsInputStreamFactory.hpp></span></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC41" 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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="nf" style="color: #900; font-weight: 600;">updateHeader</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC42" 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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arginfo</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC43" 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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamHeader</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</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="235" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -239,14 +235,6 @@ int bammerge(libmaus2::util::ArgInfo const & arginfo)</td>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp">          <span class="n" style="color: #333;">Pindex</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</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="n" style="color: #333;">indexfilename</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// need a explicit call to disconnect to avoid atexit deallocation problems in iRODS 4.19+</span></span>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">defaultIrodsSystem</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp">  <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp">                  <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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getDefaultIRodsSystem</span><span class="p">())</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">disconnect</span><span class="p">();</span></span>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC238" 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>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -254,19 +242,8 @@ int main(int argc, char * argv[])</td>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">try</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp">  <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp">          <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>

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<pre style="margin: 0;">-<span id="LC258" 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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsInputStreamFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">registerHandler</span><span class="p">();</span></span>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp">                <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC245" 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>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp">          <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>

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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// set program name for iRODS identification</span></span>

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<pre style="margin: 0;">-<span id="LC265" 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;">stringstream</span> <span class="n" style="color: #333;">irods_id</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp">          <span class="n" style="color: #333;">irods_id</span>  <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PACKAGE_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;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getProgFileName</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">progname</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;">PACKAGE_VERSION</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp">          <span class="n" style="color: #333;">setenv</span><span class="p">(</span><span class="n" style="color: #333;">SP_OPTION</span><span class="p">,</span> <span class="n" style="color: #333;">irods_id</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp">          <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); 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="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="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 old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

271

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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">

248

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<pre style="margin: 0;"> <span id="LC248" 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 old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

272

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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">

249

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<pre style="margin: 0;"> <span id="LC249" 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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<br>

</li>

<li id="be752f41aab032268ccb172abc929cf063a40400">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#be752f41aab032268ccb172abc929cf063a40400"><strong>src/programs/bamtofastq.cpp</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -761,7 +761,7 @@ void bamtofastqCollating(</td>

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<td class="diff-line-num old_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="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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<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp">                          <span class="p">}</span></span>

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<td class="diff-line-num old_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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<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>

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<td class="diff-line-num old_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

763

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<td class="diff-line-num new_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

763

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<pre style="margin: 0;"> <span id="LC763" class="line" lang="cpp">                          <span class="n" style="color: #333;">AOS</span><span class="p">[</span><span class="n" style="color: #333;">rgfshift</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">O2map</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></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="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

764

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<td class="diff-line-num new_line old" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC764" class="line" lang="cpp">                          <span class="n" style="color: #333;">filefrags</span><span class="p">[</span><span class="n" style="color: #333;">rgfshift</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Omap</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

764

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<pre style="margin: 0;">+<span id="LC764" class="line" lang="cpp">                          <span class="n" style="color: #333;">filefrags</span><span class="p">[</span><span class="n" style="color: #333;">rgfshift</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">O<span class="idiff left right">2</span>map</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

765

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<td class="diff-line-num new_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

765

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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

766

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<td class="diff-line-num new_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

766

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<pre style="margin: 0;"> <span id="LC766" 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 old_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

767

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<td class="diff-line-num new_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

767

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<pre style="margin: 0;"> <span id="LC767" class="line" lang="cpp">                          <span class="n" style="color: #333;">cnt</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="1240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1240,29 +1240,14 @@ void bamtofastq(libmaus2::util::ArgInfo const & arginfo)</td>

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1240

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<td class="diff-line-num new_line" data-linenumber="1240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1240

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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="cpp"> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1241

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<td class="diff-line-num new_line" data-linenumber="1241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1241

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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1242

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<td class="diff-line-num new_line" data-linenumber="1242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1242

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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1243

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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1243" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1244

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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1244" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/irods/IRodsInputStreamFactory.hpp></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1245

</td>

<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1245" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1246

</td>

<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1246" class="line" lang="cpp"></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="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1247

</td>

<td class="diff-line-num new_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1243

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

<pre style="margin: 0;"> <span id="LC1243" 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>

</td>

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<td class="diff-line-num old_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1248

</td>

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

1244

</td>

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

<pre style="margin: 0;"> <span id="LC1244" 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="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1249

</td>

<td class="diff-line-num new_line" data-linenumber="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1245

</td>

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

<pre style="margin: 0;"> <span id="LC1245" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</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="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1250

</td>

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

1246

</td>

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

<pre style="margin: 0;"> <span id="LC1246" class="line" lang="cpp"> <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="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1251

</td>

<td class="diff-line-num new_line old" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1251" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1252

</td>

<td class="diff-line-num new_line old" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1252" 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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsInputStreamFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">registerHandler</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1253

</td>

<td class="diff-line-num new_line old" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1253" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1254

</td>

<td class="diff-line-num new_line old" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1254" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1255

</td>

<td class="diff-line-num new_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1247

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

<pre style="margin: 0;"> <span id="LC1247" 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;">timing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RealTimeClock</span> <span class="n" style="color: #333;">rtc</span><span class="p">;</span> <span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1256

</td>

<td class="diff-line-num new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1248

</td>

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

<pre style="margin: 0;"> <span id="LC1248" class="line" lang="cpp"></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="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1257

</td>

<td class="diff-line-num new_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1249

</td>

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

<pre style="margin: 0;"> <span id="LC1249" 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="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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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1258

</td>

<td class="diff-line-num new_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1250

</td>

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

<pre style="margin: 0;"> <span id="LC1250" class="line" lang="cpp"></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="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1259

</td>

<td class="diff-line-num new_line old" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1259" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</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="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1260

</td>

<td class="diff-line-num new_line old" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1260" class="line" lang="cpp">         <span class="c1" style="color: #998; font-style: italic;">// set program name for iRODS identification</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="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1261

</td>

<td class="diff-line-num new_line old" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1261" 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;">stringstream</span> <span class="n" style="color: #333;">irods_id</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="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1262

</td>

<td class="diff-line-num new_line old" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1262" class="line" lang="cpp">         <span class="n" style="color: #333;">irods_id</span>  <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PACKAGE_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;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getProgFileName</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">progname</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;">PACKAGE_VERSION</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="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1263

</td>

<td class="diff-line-num new_line old" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1263" class="line" lang="cpp">         <span class="n" style="color: #333;">setenv</span><span class="p">(</span><span class="n" style="color: #333;">SP_OPTION</span><span class="p">,</span> <span class="n" style="color: #333;">irods_id</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1264

</td>

<td class="diff-line-num new_line old" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1264" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1265

</td>

<td class="diff-line-num new_line old" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1265" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1266

</td>

<td class="diff-line-num new_line" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1251

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<pre style="margin: 0;"> <span id="LC1251" 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 old_line" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1267

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<td class="diff-line-num new_line" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1252

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<pre style="margin: 0;"> <span id="LC1252" 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 old_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1268

</td>

<td class="diff-line-num new_line" data-linenumber="1253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1253

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<pre style="margin: 0;"> <span id="LC1253" 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>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); 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="1354" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1369,14 +1354,6 @@ int main(int argc, char * argv[])</td>

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<td class="diff-line-num old_line" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1369

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<td class="diff-line-num new_line" data-linenumber="1354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1354

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<pre style="margin: 0;"> <span id="LC1354" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1370

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<td class="diff-line-num new_line" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1355

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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="cpp">         <span class="n" style="color: #333;">bamtofastq</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1371

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<td class="diff-line-num new_line" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1356

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

<pre style="margin: 0;"> <span id="LC1356" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1372

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<td class="diff-line-num new_line old" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1372" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1373

</td>

<td class="diff-line-num new_line old" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1373" class="line" lang="cpp">         <span class="c1" style="color: #998; font-style: italic;">// need a explicit call to disconnect to avoid atexit deallocation problems in iRODS 4.19+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1374

</td>

<td class="diff-line-num new_line old" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1374" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">defaultIrodsSystem</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1375

</td>

<td class="diff-line-num new_line old" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1375" class="line" lang="cpp">         <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1376

</td>

<td class="diff-line-num new_line old" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1376" class="line" lang="cpp">                         <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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getDefaultIRodsSystem</span><span class="p">())</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">disconnect</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1377

</td>

<td class="diff-line-num new_line old" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1377" class="line" lang="cpp">         <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1378

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<td class="diff-line-num new_line old" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1378" class="line" lang="cpp">         <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1379

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<td class="diff-line-num new_line old" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1379" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1380

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<td class="diff-line-num new_line" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1357

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<pre style="margin: 0;"> <span id="LC1357" 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;">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;">MemUsage</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" wall clock time "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">formatTime</span><span class="p">(</span><span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">getElapsedSeconds</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>

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<pre style="margin: 0;"> <span id="LC1358" class="line" lang="cpp"> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC1359" 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>

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<br>

</li>

<li id="5996963c0b0cac34c60d4ecc66918c31b32d6518">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#5996963c0b0cac34c60d4ecc66918c31b32d6518"><strong>src/programs/blastnxmltobam.cpp</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,7 +54,7 @@ static std::string stripAfterSpace(std::string const & s)</td>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">XercesUtf8Transcoder</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">XercesUtf8Transcoder</span> <span class="n" style="color: #333;">this_type</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;"><span class="idiff left">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">this_type</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>::</span></span><span class="n" style="color: #333;"><span class="idiff right">type</span></span> <span class="n" style="color: #333;">unique_ptr_type</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">this_type</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">></span></span> <span class="n" style="color: #333;">unique_ptr_type</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp">   <span class="n" style="color: #333;">xercesc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">XMLTransService</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ts</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); 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="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">   <span class="n" style="color: #333;">xercesc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">XMLTranscoder</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">utf8transcoder</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); 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="1136" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1136,12 +1136,12 @@ int main(int argc, char * argv[])</td>

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<pre style="margin: 0;"> <span id="LC1136" 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;">reffn</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;">at</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="LC1137" 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;">queriesfn</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;">at</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1138" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC1139" class="line" lang="cpp">                 <span class="n" style="color: #333;"><span class="idiff left">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">bambam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">CramRange</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>::</span></span><span class="n" style="color: #333;"><span class="idiff right">type</span></span> <span class="n" style="color: #333;">Pranges</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="cpp">                 <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">bambam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">CramRange</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">></span></span> <span class="n" style="color: #333;">Pranges</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1140" 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;">CramRange</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ranges</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1141" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1142" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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;">"range"</span><span class="p">)</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC1144" class="line" lang="cpp">                         <span class="n" style="color: #333;"><span class="idiff left">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">bambam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">CramRange</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>::</span></span><span class="n" style="color: #333;"><span class="idiff right">type</span></span> <span class="n" style="color: #333;">Tranges</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1144" class="line" lang="cpp">                         <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">bambam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">CramRange</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">></span></span> <span class="n" style="color: #333;">Tranges</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1145" class="line" lang="cpp">                                 <span class="k" style="font-weight: 600;">new</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;">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;">CramRange</span><span class="o" style="font-weight: 600;">></span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1146" class="line" lang="cpp">                         <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1147" class="line" lang="cpp">                         <span class="n" style="color: #333;">Pranges</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;">move</span><span class="p">(</span><span class="n" style="color: #333;">Tranges</span><span class="p">);</span></span>

</pre>

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<br>

</li>

<li id="ab5115e6c5d8836f3f68486cbaf80c86d2df924f">

<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/eed8557fd96834ac16ad973c373d3786af6ceee2...bfc5cd7ddba5296ecd53e854866fa356808e0a22#ab5115e6c5d8836f3f68486cbaf80c86d2df924f"><strong>src/programs/fastaselectreg.cpp</strong></a>

<hr>

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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>

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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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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;">    biobambam2</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) 2020 German Tischler</span></span>

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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 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">

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

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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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<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">

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

8

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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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<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="cpp"></span>

</pre>

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

10

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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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<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">

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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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<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

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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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<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

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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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14

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

</pre>

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<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">

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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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<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">

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>

</pre>

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<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

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

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>

</pre>

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<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">

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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/util/ArgParser.hpp></span></span>

</pre>

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<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">

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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/fastx/StreamFastAReader.hpp></span></span>

</pre>

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<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">

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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/PlainOrGzipStream.hpp></span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" 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="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="cp" style="color: #999; font-weight: 600;">#include <regex></span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/lz/GzipOutputStream.hpp></span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC31" 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;">getDefaultLineLength</span><span class="p">()</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">80</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC36" 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="LC37" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * read a FastA file (possibly gziped) from stdin, select sequences with (short)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * names matching a given regular expression (argument, Posix extended regex)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * and output selected sequences on stdout (gziped if -g or --gzip is set).</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" 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="LC41" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Options:</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - singleline: output a single line of sequence data per record (i.e. do not wrap)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - longname: do not shorten the sequence name line</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - dataonly: output data only, drop FastA headers (lines starting with >)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - up: transform all sequence symbols to upper case</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - gzip: compress output using gzip</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - verbose: print which sequences are kept and which are discarded</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - l<len>: wrap sequence lines after this number of symbols (default 80)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" 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="LC50" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">fastaselectreg</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;">ArgParser</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arg</span><span class="p">)</span></span>

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

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<pre style="margin: 0;">+<span id="LC52" 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;">PlainOrGzipStream</span> <span class="n" style="color: #333;">POS</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>

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<pre style="margin: 0;">+<span id="LC53" 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;">StreamFastAReaderWrapper</span> <span class="n" style="color: #333;">SFA</span><span class="p">(</span><span class="n" style="color: #333;">POS</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC54" 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;">StreamFastAReaderWrapper</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pattern_type</span> <span class="n" style="color: #333;">pattern</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC55" 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;">linelength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">uniqueArgPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"l"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">getUnsignedNumericArg</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="p">(</span><span class="s" style="color: #d14;">"l"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">getDefaultLineLength</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC56" 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;">regex</span> <span class="n" style="color: #333;">reg</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">[</span><span class="mi" style="color: #099;">0</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;">regex_constants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extended</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC58" 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;">singleline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"s"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"singleline"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC59" 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;">longname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"L"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"longname"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC60" 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;">dataonly</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"d"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"dataonly"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" 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;">up</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"u"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"toupper"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="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;">gzip</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"g"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"gzip"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" 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;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" 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;">GzipOutputStream</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;">gzptr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC66" 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;">ostr</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;">cout</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">gzip</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">   <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 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;">GzipOutputStream</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;">tgzptr</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;">GzipOutputStream</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp">           <span class="n" style="color: #333;">gzptr</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;">move</span><span class="p">(</span><span class="n" style="color: #333;">tgzptr</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">   <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" 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;">OSI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzptr</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gzptr</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ostr</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="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">SFA</span><span class="p">.</span><span class="n" style="color: #333;">getNextPatternUnlocked</span><span class="p">(</span><span class="n" style="color: #333;">pattern</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="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="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" 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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">spat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">spattern</span><span class="p">;</span></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">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"></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">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">up</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

78

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<pre style="margin: 0;">+<span id="LC78" 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;">spat</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="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="n" style="color: #333;">spat</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;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">spat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new 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="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;">shortname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern</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="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>

</pre>

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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="k" style="font-weight: 600;">if</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;">regex_match</span><span class="p">(</span><span class="n" style="color: #333;">shortname</span><span class="p">,</span><span class="n" style="color: #333;">reg</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="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="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp">                   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">verbose</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

86

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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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[K] keeping "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">shortname</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="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

87

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

88

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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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">longname</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="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">

89

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp">                           <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">sid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shortname</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="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

90

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"></span>

</pre>

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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">

91

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">                   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">dataonly</span> <span class="p">)</span></span>

</pre>

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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 class="n" style="color: #333;">OSI</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">spattern</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="n" style="color: #333;">pattern</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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</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="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">singleline</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="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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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp">                           <span class="n" style="color: #333;">OSI</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pattern</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

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<pre style="margin: 0;">+<span id="LC95" 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">

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp">                           <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">printMultiLine</span><span class="p">(</span><span class="n" style="color: #333;">OSI</span><span class="p">,</span><span class="n" style="color: #333;">linelength</span><span class="p">);</span></span>

</pre>

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<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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<pre style="margin: 0;">+<span id="LC97" 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="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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<pre style="margin: 0;">+<span id="LC98" 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 class="n" style="color: #333;">verbose</span> <span class="p">)</span></span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp">           <span class="p">{</span></span>

</pre>

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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="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;">"[K] discarding "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">shortname</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="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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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>

</pre>

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<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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<pre style="margin: 0;">+<span id="LC104" 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="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<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>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="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 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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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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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="k" style="font-weight: 600;">try</span></span>

</pre>

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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 class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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<pre style="margin: 0;">+<span id="LC111" 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;">ArgParser</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">arg</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>

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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

113

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<pre style="margin: 0;">+<span id="LC113" 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="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp">                  <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">uniqueArgPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"v"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">uniqueArgPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"version"</span><span class="p">)</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">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp">          <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp">          <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" 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 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="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<pre style="margin: 0;">+<span id="LC118" 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="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

120

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<pre style="margin: 0;">+<span id="LC120" 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="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

121

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp">                  <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">uniqueArgPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"h"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">uniqueArgPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</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="mi" style="color: #099;">1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp">          <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp">          <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="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="125" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC125" 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="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="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;">"usage: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">arg</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;">" <regex> <in.fasta > out.fasta"</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="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="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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<pre style="margin: 0;">+<span id="LC128" 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;">"options:"</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="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">

129

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<pre style="margin: 0;">+<span id="LC129" 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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"></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="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 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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<pre style="margin: 0;">+<span id="LC132" 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="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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<pre style="margin: 0;">+<span id="LC133" 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;">"-v/--version"</span><span class="p">,</span> <span class="s" style="color: #d14;">"print version number and quit"</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">

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<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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<pre style="margin: 0;">+<span id="LC134" 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;">"-h/--help"</span><span class="p">,</span> <span class="s" style="color: #d14;">"print help message and quit"</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">

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<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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<pre style="margin: 0;">+<span id="LC135" 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;">"-l<cols>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"line length (default: "</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;">getDefaultLineLength</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="p">);</span></span>

</pre>

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<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;">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;">"-s/--singleline"</span><span class="p">,</span> <span class="s" style="color: #d14;">"do not wrap sequence data lines"</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="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;">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;">"-L/--longname"</span><span class="p">,</span> <span class="s" style="color: #d14;">"do not shorten name"</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="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;">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;">"-d/--dataonly"</span><span class="p">,</span> <span class="s" style="color: #d14;">"do not print FastA header (data 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="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="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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<pre style="margin: 0;">+<span id="LC139" 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;">"-u/--toupper"</span><span class="p">,</span> <span class="s" style="color: #d14;">"convert sequence symbols to upper case"</span> <span class="p">)</span> <span class="p">);</span></span>

</pre>

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</td>

<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 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;">"-g/--gzip"</span><span class="p">,</span> <span class="s" style="color: #d14;">"compress output"</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="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>

</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">

</td>

<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

</td>

<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="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>

</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

</td>

<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>

</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">

</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

</td>

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

<pre style="margin: 0;">+<span id="LC144" 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>

</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="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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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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

</td>

<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>

</pre>

</td>

</tr>

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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="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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<pre style="margin: 0;">+<span id="LC147" 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="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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

</td>

</tr>

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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 class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fastaselectreg</span><span class="p">(</span><span class="n" style="color: #333;">arg</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC150" 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="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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC151" 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>

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

<pre style="margin: 0;">+<span id="LC152" 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="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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC153" 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>

</td>

</tr>

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

<pre style="margin: 0;">+<span id="LC154" 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>

</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">

</td>

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

<pre style="margin: 0;">+<span id="LC155" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"><span class="p">}</span></span></pre>

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